Method and system for depleting rRNA populations

ABSTRACT

The present invention concerns a system for isolating, depleting, or separating a targeted nucleic acid, such as rRNA, from a sample comprising targeted and nontargeted nucleic acids. It effects a way of enriching for nontargeted nucleic acids, such as mRNAs. The invention further concerns methods of implementing the system and kits for implementing the system, which involves at least one bridging nucleic acid comprising 1) a targeting region complementary to a region on the targeted nucleic acid and 2) a bridging region complementary to the capture region of a capture nucleic acid that comprises a nonreactant structure. The nonreactant structure can be used to isolate the hybridizing molecules after incubation under conditions that allows hybridization.

BACKGROUND OF THE INVENTION

[0001] 1. Field of the Invention

[0002] The present invention relates generally to the fields of molecular biology and microbial pathogenesis. More particularly, it concerns methods, compositions, and kits for isolating, depleting, separating a targeted nucleic acid population from other nucleic acid populations as a means for enriching those other nucleic acid population(s). More particularly, it concerns methods, compositions, and kits for enriching mRNA populations by depleting eukaryotic and/or prokaryotic rRNA from a sample using engineered bridging and capture nucleic acid molecules.

[0003] 2. Description of Related Art

[0004] The ongoing efforts in microbial genome sequencing will enable unprecedented advances in our understanding of microbes and host-microbe interactions. Dozens of prokaryotic genomes, including those of numerous human pathogens, have been completely sequenced, and many others are in progress. Consequently, a renewal of focus and energy has emerged in the fields of microbial evolution, microbial pathogenesis, and infectious diseases. The potential impact of genomics on these disciplines is the subject of several recent reviews (Cummings et al., 2000; Cornelis et al., 2001; Fox et al., 2001; Current Opinion in Microbiology). For host-microbe interactions, the ability to measure the expression of every single gene in a microorganism will make possible studies of such complex interactions as the global regulation of virulence factors and the mechanisms of response to host cells and their microenvironment. Scientists will also be able to evaluate the complete repertoire of host cell gene expression in response to the pathogen. Undoubtedly, novel interactions and responses between microbes and their hosts will be discovered, leading to a more complete picture of infectious diseases and how to control them.

[0005] In the past decade, researchers studying bacteria developed several novel approaches to evaluate global gene transcription in response to environmental stimuli, including host-microbe interactions. Prior to the era of genome sequencing, Chuang et al. (Chuang et a., 1993) used an ordered set of E. coli lambda library clones to evaluate global transcription responses of E. coli. Other groups employed subtractive hybridization and differential screening to evaluate induction of gene expression in Mycobacterium avium after phagocytosis by macrophages (Plum et al., 1994) or in Pyrococcus grown under specific environmental conditions (Robinson et al., 1994). Researchers further developed this approach with an elegant procedure for the selective capture of transcribed sequences (SCOTS) (Graham et al., 1999). At the same time, many scientists bypassed library construction altogether and used using differential display (Liang et al., 1995) to discover genes that are transcribed differently under various growth conditions. Although useful in certain circumstances, differential display is frequently a hit-or-miss prospect and gives no information on global transcription. More recently, serial analysis of gene expression (SAGE) (Velculescu et al., 1995) emerged as a method for analyzing the complete transcriptome of a cell. SAGE, like differential display, can be useful but requires large amounts of nucleic acid sequencing. Not unexpectedly, for organisms whose genomes have been sequenced, array analysis is emerging as the method of choice for global gene expression studies with bacteria. Macroarrays (filter-based arrays) and microarrays (slide-based arrays) of complete genomes have made possible the simultaneous expression analysis of thousands of genes. The advent of microarray technology has already enabled analyses of the host response to interactions with pathogenic organisms (Cummings et al., 2000). Similarly, microarray analysis and other methods have been used to evaluate gene expression in bacteria grown under different environmental conditions in vitro.

[0006] The application of array analysis to gene expression profiling in prokaryotes was an immediate outgrowth of similar studies with eukaryotic organisms, occurring only within the past two to three years. Infectious disease researchers have already begun applying microarray analysis to the study of complex host-microbe interactions. To date, such analyses of host-microbe interactions have been limited to the evaluation of host cell responses to bacteria or viruses. Bordetella pertussis, Listeria monocytogenes, Neisseria meningitidis, Pseudomonas aeruginosa, Legionella pneumophila, Salmonella dublin, and Staphylococcus aureus are among the bacterial pathogens whose effects on host cell gene expression have been evaluated with microarrays. Array analyses of eukaryotic host cell transcription are feasible because of the ability to isolate polyadenylated mRNAs from eukaryotic cells and to specifically label mRNAs by oligo dT-primed cDNA synthesis.

[0007] Although it has been alluded to in the literature (Cummings et al, 2000; Rappuoli, 2000), complete genome array expression analyses of bacteria in response to interactions with host cells have not been widely published, if at all. Studies that examine the global bacterial gene response in the presence of host cells will require the development of tools to enable the efficient isolation, enrichment, and labeling of bacterial mRNAs (Cummings et al., 2000; Graham et al., 1999; Gingeras et al., 2000; Graham et al., 2001).

[0008] However, technical limitations of current methods available for purification and evaluation of bacterial mRNAs preclude these types of whole genome analysis. To realize the full potential of the genomics revolution, methods for purifying mRNAs from total bacterial RNA populations and particularly from mixtures of host cell and bacterial RNA need to be developed.

[0009] Isolating sufficient quantities of high quality bacterial mRNA is perhaps the most demanding technical requirement impeding analyses of bacterial gene expression in the presence of host cells. A small percentage of bacterial mRNAs may be A-tailed, but these are targeted for degradation and tend to be unstable. As a result, the commonly used method for mRNA purification with eukaryotic cells, oligo-dT capture, is ineffective.

[0010] Only a few studies have described methods for enriching or purifying bacterial mRNAs. Several groups (Plum et al., 1994; Robinson et al., 1994; Su et al., 1998) have used rRNA subtraction to enrich for bacterial mRNAs. These procedures involved hybridization of rRNAs to biotinylated plasmid containing rRNA genes or to biotinylated antisense rRNAs followed by streptavidin capture and removal. This yields some benefits, but it requires fairly large amounts of plasmids or antisense RNA. Biotinylation of large amounts of DNA or RNA is often tricky and can be prohibitively expensive if biotin-modified nucleotides are incorporated during antisense RNA synthesis. In general, these methods have not seen widespread use. As mentioned above, Graham and Clarke-Curtiss (Graham et al., 1999) went further in enriching for mycobacterial mRNAs with SCOTS. The SCOTS procedure is effective for detecting genes specifically expressed in the presence of host cells but is hampered by being a multi-step procedure that requires production of normalized double-stranded cDNA, PCR, differential hybridization, and cDNA capture. In addition to these methods, researchers have developed methods to polyadenylate bacterial mRNAs, thereby allowing for their purification by oligo dT-capture. Amara and Vijaya (Amara et al., 1997) demonstrated that mRNAs in purified polysomes can be specifically polyadenylated and purified by oligo-dT capture. Wendisch et al. (Wendisch et al., 2001) showed that the same process can be carried out with crude cell extracts. Several shortcomings are associated with the polyadenylation approach. Different mRNAs may be polyadenylated to different extents or not at all depending on the structure of their 5′ and 3′ ends (Feng et al., 2000). Polyadenylation in a cell lysate, followed by purification of RNA, will require inactivation of cellular RNAses so that transcripts are not degraded during the polyadenylation reaction. Optimizing the reaction to work reproducibly in many different bacterial cell lysates would likely be very difficult. Despite many worthy attempts, simple and universal procedures for bacterial mRNA enrichment, especially in the presence of host cell RNA, remain elusive. Thus, there remains a continued need for improvements in mRNA enrichment and/or the depletion of other RNA populations.

SUMMARY OF THE INVENTION

[0011] The present invention involves a system that allows for the isolation, separation, and depletion of a population of nucleic acid molecules. The system involves components that may be used to implement methods for isolating, separating, or depleting a targeted nucleic acid. Such components may also be included in kits of the invention.

[0012] In embodiments of the invention, a population of nucleic acids may be targeted for isolation, separation, or depletion. Such a nucleic acid is referred to as “targeted nucleic acid” or “targeted nucleic acid molecule.” Alternatively, it may be referred to as a “nucleic acid target.” In particular embodiments of the invention, the targeted nucleic acid is rRNA. In alternative embodiments, the targeted nucleic acid is mRNA, tRNA, or DNA including, cDNA and genomic DNA. The targeted nucleic acid may be in a sample, which is a composition that is suspected of containing the targeted nucleic acid. In some embodiments, the sample is obtained from or includes prokaryotes or eukaryotes or both. The sample may be cells, tissues, organs, and lysates, fractionations, or portions thereof. Furthermore, the targeted nucleic acid is targeted via a “targeting region” in the targeted nucleic acid. A “targeted region” refers to a region of the targeted nucleic acid that is complementary with the targeting region of a bridging nucleic acid and that allows the targeted nucleic acid to be separated from other non-targeted nucleic acid populations.

[0013] In embodiments in which the targeted nucleic acid is rRNA, the rRNA may be the SS, 16S, or 23S rRNA from prokaryotes, though it may be any rRNA species from a prokaryotes. It is specifically contemplated that nucleic acids may be targeted in Gram positive bacteria and Gram negative bacteria. In further embodiments, the targeted rRNA is 5.8S, 17S or 18S, or 28S rRNA (referred to as “types of rRNA”) from a eukaryote. It is further contemplated that tRNA may be a targeted nucleic acid population either by itself or in combination with any of the targeted nucleic acids described herein. A non-limiting list of targeted rRNAs from various organisms is provided in a later section and is contemplated to be part of the invention.

[0014] In embodiments of the invention, the system involves a bridging nucleic acid, a capture nucleic acid, and a targeted nucleic acid, as shown, for example, in FIG. 1. While in many embodiments of the invention it is contemplated that the bridging nucleic acid and the capture nucleic acid are oligonucleotides, it is specifically contemplated that they may be polynucleotides as well. Thus, any embodiment involving an oligonucleotide may be implemented with a polynucleotide. Bridging nucleic acids, capture nucleic acids, and targeted nucleic acids of the invention may include, be at least or be at most 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 210, 220, 230, 240, 250, 260, 270, 280, 290, 300, 310, 320, 330, 340, 350, 360, 370, 380, 390, 400, 410, 420, 430, 440, 450, 460, 470, 480, 490, 500, 510, 520, 530, 540, 550, 560, 570, 580, 590, 600, 610, 620, 630, 640, 650, 660, 670, 680, 690, 700, 710, 720, 730, 740, 750, 760, 770, 780, 790, 800, 810, 820, 830, 840, 850, 860, 870, 880, 890, 900, 910, 920, 930, 940, 950, 960, 970, 980, 990, 1000 or more residues in length.

[0015] Furthermore, a “bridging nucleic acid” is a nucleic acid molecule that comprises a bridging region and a targeting region, while a “capture nucleic acid” is a nucleic acid molecule that comprises a capture region. It is contemplated that bridging, targeting, and capture regions of the invention may be, be at least or be at most 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 210, 220, 230, 240, 250, 260, 270, 280, 290, 300, 310, 320, 330, 340, 350, 360, 370, 380, 390, 400, 410, 420, 430, 440, 450, 460, 470, 480, 490, 500, 510, 520, 530, 540, 550, 560, 570, 580, 590, 600, 610, 620, 630, 640, 650, 660, 670, 680, 690, 700, 710, 720, 730, 740, 750, 760, 770, 780, 790, 800, 810, 820, 830, 840, 850, 860, 870, 880, 890, 900, 910, 920, 930, 940, 950, 960, 970, 980, 990, or 1000 residues in length.

[0016] A “bridging nucleic acid” refers to a molecule that includes nucleic acid residues or analogs and that includes at least one targeting region and at least one bridging region. A “targeting region” refers to a region of the molecule that is involved in targeting a particular nucleic acid or nucleic acid population and is thus complementary to all or part of the sequence of the targeted nucleic acid. It is further contemplated that more than one targeting region may be included in a bridging nucleic acid. The bridging nucleic acid may include or have up to 2, 3, 4, 5, 6, 7, 8, 9, 10, or more targeting regions. When there are multiple targeting regions, it is contemplated that the regions may be complementary to different, nonoverlapping sequences from the same targeted nucleic acid or they may be complementary to similar or overlapping sequences from the same targeted nucleic acid, or they may be complementary to sequences in different targeted nucleic acids. While mRNA may be targeted, it is specifically contemplated that mRNA is not targeted and thus the targeting region does not have a stretch of polypyrimidine residues, such as poly-T or poly-U to hybridize to the poly-A tail of eukaryotic mRNA. Also considered part of the invention is using single or multiple bridging nucleic acids to deplete an rRNA population. In some embodiments, a single bridging nucleic acid may contain one or more targeting regions that are complementary to different types of rRNA (“types” refer to sizes based on intact lengths). Thus, in some embodiments, the largest type of rRNA may be targeted (“largest” refers to longest nucleic acid molecule when intact, even though molecules that are no longer intact may also be targeted if they retain the sequence that is complementary to all or part of a targeting region). In still further embodiments, the second largest rRNA or the first and second largest rRNA types may be targeted by a single bridging nucleic acid with targeting regions to each or to more than one nucleic acid, each with a targeting region to a different type of rRNA. In still further embodiments, a bridging nucleic acid has a targeting region complementary to one or more of the following prokaryotic and eukaryotic rRNA types: 5S, 16S, 23S, 5.8S, 17S, 18S, and/or 28S. A bridging nucleic acid may target 1, 2, 3, 4, 5, 6, 7, or more types of rRNA, as well as any and all tRNA types, both eukaryotic and prokaryotic.

[0017] A “bridging region” in a bridging nucleic acid refers to a region that mediates an interaction with a capture nucleic acid. In further embodiments, the bridging region is a polypurine or polypyrimidine stretch of residues. A bridging region can include a stretch of adenine or guanine residues or cytosine, uracil, or thymidine residues. In some embodiments, it is contemplated that more than one bridging region is included in a bridging nucleic acid, such as 2, 3, 4, 5, or more bridging regions.

[0018] A “capture nucleic acid” refers to a molecule that includes nucleotides or nucleotide analogs, a capture region, and a nonreacting structure. A “capture region” refers to a region that interacts with the bridging region of a bridging nucleic acid. In embodiments of the invention, the bridging region and the capture region are complementary to each other and hybridize to one another under conditions that allow for hybridization of complementary regions. There may be more than one nonreacting structure attached, covalently or noncovalently, to a capture nucleic acid. There may be 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more nonreacting structures as part of a capture nucleic acid.

[0019] A capture nucleic acid also includes a “nonreacting structure,” which refers to a compound that does not chemically react with a nucleic acid. In some embodiments, a nonreacting structure is a magnetic bead or rod, which allows the capture nucleic acid, a bridging nucleic acid and a target nucleic acid to be isolated from a sample with a magnetic field, such as a magnetic stand. In still further embodiments, the nonreacting structure is a bead or other structure that can be physically captured, such as by using a basket, filter, or by centrifugation. It is contemplated that a bead may include plastic, glass, teflon, silica, a magnet or be magnetizeable, a metal such as a ferrous metal or gold, carbon, cellulose, latex, polystyrene, and other synthetic polymers, nylon, cellulose, nitrocellulose, polymethacrylate, polyvinylchloride, styrene-divinylbenzene, or any chemically-modified plastic or any other nonreacting structure. In still further embodiments, the nonreacting structure is biotin or iminobiotin. Biotin or iminobiotin binds to avidin or streptavidin, which can be used to isolate the capture nucleic acid and any hybridizing molecules. Furthermore, in some embodiments of the invention, the nonreacting structure is cellulose or an analog thereof.

[0020] It is contemplated that the location of the targeting and bridging regions in the bridging nucleic acid may be at a variety of positions. The location of targeted regions in a targeted nucleic acid or a capture region in a capture nucleic acid may also vary. The location of any of these regions or nonreacting structure may be or be within 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 12, 130, 140, 150, 160, 170, 180, 190, 200, 210, 220, 230, 240, 250, 260, 270, 280, 290, 300, 310, 320, 330, 340, 350, 360, 370, 380, 390, 400, 410, 420, 430, 440, 450, 460, 470, 480, 490, 500, 510, 520, 530, 540, 550, 560, 570, 580, 590, 600, 610, 620, 630, 640, 650, 660, 670, 680, 690, 700, 710, 720, 730, 740, 750, 760, 770, 780, 790, 800, 810, 820, 830, 840, 850, 860, 870, 880, 890, 900, 910, 920, 930, 940, 950, 960, 970, 980, 990, 1000, 1100, 1200, 1300, 1400, 1500, 1600, 1700, 1800, 1900, 2000, 2100, 2200, 2300, 2400, 2500, 2600, 2700, 2800, 2900, 3000, 3100, 3200, 3300, 3400, 3500, 3600, 3700, 3800, 3900, 4000, 4100, 4200, 4300, 4400, 4500, 4600, 4700, 4800, 4900, 5000 or more nucleotides from the 3′ and/or 5′ end of the relevant nucleic acid (“relevant nucleic acid” refers to the nucleic acid in which the region is located). Moreover, it is contemplated that a region, such as a bridging, capture, targeted, or targeting region-as well as a nonreacting structure-may be at or within 100-5000 residues, 150-4000 residues, 200-3000 residues, 250-2000 residues, 300-1500 residues, 350-1000 residues, 400-900 residues, 450-800 residues, or 500-700 residues of the 5′ or 3′ end of the relevant nucleic acid.

[0021] Furthermore, it is also contemplated that the spacing between regions may vary. Regions in the same nucleic acid or a region and a nonreacting structure may be adjacent to one another or there may be residues between them or between each of them. The number of intervening residues may be the following or may be at least or at most of the following: 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 210, 220, 230, 240, 250, 260, 270, 280, 290, 300, 310, 320, 330, 340, 350, 360, 370, 380, 390, 400, 410, 420, 430, 440, 450, 460, 470, 480, 490, 500, 510, 520, 530, 540, 550, 560, 570, 580, 590, 600, 610, 620, 630, 640, 650, 660, 670, 680, 690, 700, 710, 720, 730, 740, 750, 760, 770, 780, 790, 800, 810, 820, 830, 840, 850, 860, 870, 880, 890, 900, 910, 920, 930, 940, 950, 960, 970, 980, 990, 1000, 1100, 1200, 1300, 1400, 1500, 1600, 1700, 1800, 1900, 2000, 2100, 2200, 2300, 2400, 2500, or more nucleotides between them or each of them.

[0022] As for the location of the sequence to which the targeting region is complementary, termed “targeted region,” this may be 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1100, 1200, 1300, 1400, 1500, 1600, 1700, 1800, 1900, 2000, 2100, 2200, 2300, 2400, 2500, 2600, 2700, 2800, 2900, 3000, 3100, 3200, 3300, 3400, 3500, 3600, 3700, 3800, 3900, 4000, 4100, 4200, 4300, 4400, 4500, 4600, 4700, 4800, 4900, 5000 nucleotides or more from the 3′ and/or 5′ end of the targeted nucleic acid. It is specifically contemplated that the targeting region hybridizes to a sequence located between 100 and 5000, 150 and 4000, 200 and 3000, 250 and 2000, and 300 and 1000 residues of the 5′ and/or 3′ end of the targeted nucleic acid. It is also contemplated that the targeted region is at the 3′ or 5′ end of the targeted nucleic acid. Alternatively, the targeted region may not be within 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1100, 1200, 1300, 1400, 1500, 1600, 1700, 1800, 1900, 2000, 2100, 2200, 2300, 2400, 2500, 2600, 2700, 2800, 2900, 3000, 3100, 3200, 3300, 3400, 3500, 3600, 3700, 3800, 3900, 4000, 4100, 4200, 4300, 4400, 4500, 4600, 4700, 4800, 4900, 5000 or more nucleotides from the termini of a targeted nucleic acid.

[0023] In some embodiments, the targeting region comprises or is complementary to all or 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 210, 220, 230, 240, 250, 260, 270, 280, 290, 300, 310, 320, 330, 340, 350, 360, 370, 380, 390, 400, 410, 420, 430, 440, 450, 460, 470, 480, 490, 500, 510, 520, 530, 540, 550, 560, 570, 580, 590, 600, 610, 620, 630, 640, 650, 660, 670, 680, 690, 700, 710, 720, 730, 740, 750, 760, 770, 780, 790, 800, 810, 820, 830, 840, 850, 860, 870, 880, 890, 900, 910, 920, 930, 940, 950, 960, 970, 980, 990, 1000 or more contiguous nucleotides of SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:1, SEQ ID NO:12, SEQ ID NO:13, SEQ ID NO:14, SEQ ID NO:15, SEQ ID NO:16, SEQ ID NO:17, SEQ ID NO:18, SEQ ID NO:19, SEQ ID NO:20, SEQ ID NO:21, SEQ ID NO:22, SEQ ID NO:23, SEQ ID NO:24, SEQ ID NO:25, SEQ ID NO:26, SEQ ID NO:27, SEQ ID NO:28, SEQ ID NO:29, SEQ ID NO:30, SEQ ID NO:31, SEQ ID NO:32, SEQ ID NO:33, SEQ ID NO:34, SEQ ID NO:35, SEQ ID NO:36, SEQ ID NO:37, SEQ ID NO:38, SEQ ID NO:39, SEQ ID NO:40, SEQ ID NO:41, SEQ ID NO:42, SEQ ID NO:43, SEQ ID NO:44, SEQ ID NO:45, SEQ ID NO:46, SEQ ID NO:47, SEQ ID NO:48, SEQ ID NO:49, SEQ ID NO:50, SEQ ID NO:51, SEQ ID NO:52, SEQ ID NO:53, SEQ ID NO:54, SEQ ID NO:55, SEQ ID NO:56, SEQ ID NO:57, SEQ ID NO:58, SEQ ID NO:59, SEQ ID NO:60, SEQ ID NO:61, SEQ ID NO:62, SEQ ID NO:63, SEQ ID NO:64, SEQ ID NO:65, SEQ ID NO:66, SEQ ID NO:67, SEQ ID NO:68, SEQ ID NO:69, SEQ ID NO:71, SEQ ID NO:72, or SEQ ID NO:73 (collectively referred to as “SEQ ID NOS:1-73”). It is specifically contemplated that targeting regions of the invention comprise, in some embodiments, at least 5 contiguous nucleotides of SEQ ID NO:1-22; it is also contemplated that targeting regions of the invention are complementary to a sequence (“sequence” in the context of complementary regions refers to a sequence of at least 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, or more nucleotides in length) of SEQ ID NOS:23-73, which are sequences of rRNA molecules.

[0024] It will be understood that any embodiment discussed with respect to nucleotides applies also when nucleotide analogs are used. It is specifically contemplated that nucleotide analogs may be employed with respect to bridging and capture nucleic acids of the invention.

[0025] It is contemplated that nucleic acids of the invention include RNA, DNA, locked nucleic acid™ (LNA), iso-bases, and/or peptide mimetics. It is contemplated that all or part of nucleic acids of the invention may include such nucleic acid components.

[0026] The present invention further concerns methods of isolating and/or depleting nucleic acids from a sample. In some embodiments, methods include a) incubating a sample with a first bridging nucleic acid comprising (1) at least one bridging region comprising at least 5 nucleic acid residues, under conditions allowing hybridization between the first targeting region and the targeted nucleic acid; b) incubating the first bridging nucleic acid with a capture nucleic acid comprising a nonreacting structure and a capture region comprising at least 5 nucleic acid residues, under conditions that allowing hybridization between the first bridging region and the capture region. In additional embodiments, one or more other steps may be included in combination with the method discussed above. Other steps involve isolating the targeted nucleic acid from the remainder of the sample; discarding the portion of the sample that hybridizes directly or indirectly to the capture nucleic acid (indirect hybridization refers to specific association of compounds that occurs through hybridization with a mediating compound, for example, indirect hybridization of a capture nucleic acid and a targeted nucleic acid via hybridization to a bridging nucleic acid); incubating the sample with additional bridging nucleic acids, under conditions allowing hybridization between the targeting region of the additional bridging nucleic acid and the targeted nucleic acid; implementing the method with respect to other targeted nucleic acids; washing the capture nucleic acid after incubation with the sample and the bridging nucleic acid; incubating the capture nucleic acid, bridging nucleic acid, and sample with elution buffer after isolating the targeted nucleic acid from the rest of the sample; eluting the targeted nucleic acid from the nonreactant structure; using the capture nucleic acid in a subsequent method involving a new sample; discarding the targeted nucleic acid after separating it from the sample; performing hybridizations between the bridging nucleic acid and the sample and the capture nucleic acid and the sample at the same temperatures or at different temperatures; performing the above hybridization steps at the same time, sequentially (one after the other or the other after the one); exposing the sample to a magnetic field or magnet, particularly when a magnetic bead or other object comprises all or part of the nonreacting structure of the capture nucleic acid; and incubating the sample with streptavidin or avidin, particularly if biotin or iminobiotin is used as a non-reacting structure.

[0027] In some embodiments of the invention, the sample, a bridging nucleic acid and/or a capture nucleic acid are incubated in a buffer, which, in some embodiments, includes TEAC or TMAC.

[0028] In methods of the invention involving more than one bridging nucleic acid, it is contemplated that the targeting region of the first bridging nucleic acid may be complementary to a different sequence of a different targeted nucleic acid than a targeting region of another bridging nucleic acid. Alternatively, different bridging nucleic acids may have targeting regions that are complementary to the same targeted nucleic acid. In the latter case, it is further contemplated that the targeting regions be complementary to sequences that overlap one another or ma be complementary to sequences in non-overlapping locations.

[0029] In cases in which targeting regions are complementary to different targeted nucleic acids, embodiments may involve targeting the largest rRNA molecule in a sample with one bridging nucleic acid and the second largest rRNA molecule in a sample with another bridging nucleic acid. In still further embodiments, another or third bridging nucleic acid will target the third largest rRNA molecule in a sample, while another or a fourth bridging nucleic acid will target the fourth largest rRNA molecule in a sample.

[0030] In another embodiment of the invention, there is a method for depleting rRNA from a sample comprising incubating the sample with (1) at least a first bridging oligonucleotide comprising a bridging region comprising a polypurine region of at least 5 residues in length and a targeting region comprising at least 5 contiguous residues complementary to an rRNA molecule in the sample and (2) a capture oligonucleotide comprising a magnetic bead and a capture region comprising a polypyrimidine region of at least 5 residues in length, under conditions allowing hybridization between the bridging oligonucleotide and the capture oligonucleotide and between the bridging oligonucleotide and the rRNA; b) incubating the sample with a magnetic bead; and c) isolating the magnetic bead. In still further embodiments, the first bridging oligonucleotide comprises a targeting region complementary to prokaryotic 23S rRNA. In still further embodiments, there is a second bridging oligonucleotide with a targeting region complementary to a different region of a prokaryotic 23S RNA than the first bridging oligonucleotide. In even further embodiments, there is a third and fourth bridging oligonucleotide each with a targeting region complementary to different sequences of a prokaryotic 16S rRNA.

[0031] As discussed earlier, a sample may be depleted or isolated as a way of enriching for the nontargeted nucleic acid, such as mRNA. In further embodiments of the invention, enriched mRNA can be used to prepare cDNA according to methods known to those of ordinary skill in the art, and as described herein. Thus, in cases in which mRNA is enriched as a result of methods of the invention, embodiments may further include discarding the portion of the sample that hybridizes to the capture oligonucleotide. More specifically targeted rRNA may be discarded and the mRNA remaining in the sample may be used to produce cDNA molecules. cDNA molecules may be used in a variety of methods, including, but not limited to, library production, production of proteins, and for creating and screening arrays. Therefore, in some embodiments of the invention, cDNA made from mRNA enriched according to methods of the invention are attached to a solid support or surface so as to create a nucleic acid array. The term “nucleic acid array” refers to a plurality of target elements, wherein each target element comprising one or more nucleic acid molecules immobilized on one or more solid surfaces at discrete locations to which sample nucleic acids can by hybridized. The nonreacting solid surface or support may be any of a number of materials, including plastic, glass, or nylon. In some embodiments, the solid support is a plate. The plate may have wells that contain the target elements. Plates may have 2, 3, 4, 5, 6, 7, 8, 9, 10 or more wells (“multi-well”), and up to at least 96 or 192 wells. In some embodiments of the invention, the sample nucleic acids comprise cDNAs made by depleting a sample of rRNA, according to methods of the invention. Those embodiments may further involve contacting a nucleic acid array with the cDNA. Alternatively, cDNA made according to the invention may be used as target elements on an array.

[0032] The present invention also concerns kits that include compositions of the invention to implement the methods discussed herein. These kits can be used for the depletion, isolation, or purification of nucleic acids. Kits contain these compositions in a suitable container means.

[0033] In some embodiments, a kit includes 1) at least one capture oligonucleotide comprising a capture region and a magnetic bead; and 2) at least a first bridging oligonucleotide comprising i) at least one bridging region complementary to all or part of the capture region of the capture oligonucleotide and ii) at least one targeting region comprising 10 contiguous nucleic acids complementary to an rRNA.

[0034] In additional embodiments, there is a second bridging oligonucleotide comprising i) at least one bridging region complementary to all or part of the capture region of the capture oligonucleotide and ii) at least one targeting region comprising 10 contiguous nucleic acids complementary to an rRNA. In some kits, the targeting region of the second bridging oligonucleotide is complementary to the same rRNA as the targeting region of the first bridging oligonucleotide, while in other embodiments, these are complementary to different rRNAs. Further embodiments involve kits in which the targeting region of the first bridging oligonucleotide is complementary to the largest rRNA of a prokaryote or eukaryote. In other embodiments, the second bridging oligonucleotide has a targeting region that is complementary to either the largest rRNA of a prokaryote or eukaryote or the second largest rRNA of a prokaryote or eukaryote. It is specifically contemplated that kits may include one or more bridging oligonucleotides targeting prokaryotic rRNA (16S, 23S, or both) and one or more bridging oligonucleotides targeting eukaryotic rRNA (18S, 28S, or both); thus, a kit may be used for depleting both eukaryotic and prokaryotic rRNA, in some embodiments.

[0035] Kits may also include a third, fourth, fifth, sixth, seventh, eighth, ninth, tenth or more bridging oligonucleotides with targeting region complementary to the same or different rRNAs as the targeting regions of the first and second bridging oligonucleotides. It is contemplated that the targeting regions of the bridging oligonucleotides in kits of the invention may be complementary to prokaryote 16S rRNA, prokaryote 23S rRNA, prokaryote 5S rRNA, eukaryote 17S or 18S rRNA, eukaryote 28SrRNA, and/or eukaryote 5.8S rRNA. It is further contemplated that targeting regions of bridging oligonucleotides in kits may have all or part of SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12, SEQ ID NO:13, SEQ ID NO:14, SEQ ID NO:15, SEQ ID NO:16, SEQ ID NO:17, SEQ ID NO:18, SEQ ID NO:19, SEQ ID NO:20, SEQ ID NO:21, or SEQ ID NO:22 (collectively referred to as “SEQ ID NOS:1-22”). Alternatively, kits may include targeting regions as discussed above with respect to SEQ ID NOS:23-73, i.e. targeting regions complementary to a sequence from SEQ ID NOS:23-73. Kits of the invention may also include one or more of the following: binding buffer with TMAC, binding buffer with TEAC, magnetic stand, wash solution, nuclease-free water; RNAse inhibitors, glycogen, control RNA, sodium acetate, ammonium acetate, streptavidin beads, avidin beads, magnetic beads, beads of any nonreacting structure—including those discussed above—capture basket; capture filters, RNA markers, nuclease-free containers such as tubes and tips, and any other composition described herein.

[0036] It is contemplated that kits of the invention may be used to implement methods of the invention, that methods of the invention may be implemented with compositions of the invention, and that kits may include any composition of the invention.

[0037] It is further contemplated that kits, methods, and compositions of the invention may effect a depletion of a targeted nucleic acid in a sample by reducing its amount in the sample by at least 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 96, 97, 98, 99, 99.1, 99.2, 99.3, 99.4, 99.5, 99.6, 99.7, 99.8, 99.9 or more percent.

[0038] Kits of the invention also include materials for creating a nucleic acid array. Any of the kits discussed above may also include a solid support for preparing a nucleic acid array.

[0039] The use of the word “a” or “an” when used in conjunction with the term “comprising” in the claims and/or the specification may mean “one,” but it is also consistent with the meaning of “one or more,” “at least one,” and “one or more than one.” When the term “at least” is used in the context of bridging, targeting, or capture regions, as well as for capture and bridging oligonucleotides, it is contemplated that there is an upper limit of 20 for practical purposes, even though more such regions or oligonucleotides could be implemented with the invention. Furthermore, it should be understood that a number (cardinal or ordinal) used in the context of compositions of the invention refers to a “kind” of that composition; thus, “a first oligonucleotide” in the context of a “second oligonucleotide” refers to “one of that kind of oligonucleotide,” and not one single oligonucleotide molecule.

[0040] Other objects, features and advantages of the present invention will become apparent from the following detailed description. It should be understood, however, that the detailed description and the specific examples, while indicating specific embodiments of the invention, are given by way of illustration only, since various changes and modifications within the spirit and scope of the invention will become apparent to those skilled in the art from this detailed description.

BRIEF DESCRIPTION OF THE DRAWINGS

[0041] The following drawings form part of the present specification and are included to further demonstrate certain aspects of the present invention. The invention may be better understood by reference to one or more of these drawings in combination with the detailed description of specific embodiments presented herein.

[0042]FIG. 1. Depiction of molecules in system. A bridging oligonucleotide is shown with a targeting region and a bridging region. The targeting region is complementary to a targeted region in the targeted nucleic acid, which is an rRNA molecule. The bridging region is complementary to the capture region in the capture oligonucleotide, which is attached, by way of example, to a magnetic bead as a nonreacting structure.

[0043] FIGS. 2A-1 to A-14 and FIGS. 2B-1 to B-27. Sequence comparison of different rRNAs from different bacteria to E. coli rRNA with MegAlign sequence analysis software version 4.05 from DNA Star, Incorporated. A. The 5′ end of the sequence is shown on the first page of the figure in FIG. 2A-1 and continues until the last page of the figure, FIG. 2A-14, in which the 3′ end of the same sequence is shown. Shown is a sequence comparison of 16S rRNA of listed prokaryotic organisms to 16S rRNA from E. coli (SEQ ID NO:34). The sequences are the 16S rRNA from the following organisms: B. subtilis (SEQ ID NO:23); B. anthracis (SEQ ID NO. 24); E. faecalis (SEQ ID NO. 25); L. lactis (SEQ ID NO. 26); L. monocyt (SEQ ID NO. 27); S. aureus (SEQ ID NO. 28); S. mutans (SEQ ID NO. 29); S. pneumon (SEQ ID NO. 30); S. pyogenes (SEQ ID NO. 31); M. avian (SEQ ID NO. 32); M. tuberculosis (SEQ ID NO. 33); K. pneumoniae (SEQ ID NO. 35); A. actino (SEQ ID NO. 36); H. influenzae (SEQ ID NO. 37); E. bronchiseptica (SEQ ID NO. 38); B. parapertussis (SEQ ID NO. 39); B. pertussis (SEQ ID NO. 40); B. cepacia (SEQ ID NO. 41); B. mallei (SEQ ID NO. 42); B. pseudomallei (SEQ ID NO. 43); N. gonorrhoeae (SEQ ID NO. 44); N. mening (SEQ ID NO. 45); P. aeruginosa (SEQ ID NO. 46); V. cholerae (SEQ ID NO. 47); and Y. enterocolitica (SEQ ID NO. 48). B. The 5′ end of the sequence is shown on the first page of the figure in FIG. 2B-1 and continues until the last page of the figure, FIG. 2B-27, in which the 3′ end of the same sequence is shown. Shown is a sequence comparison of 23S rRNA of listed prokaryotic organisms to 23S rRNA from E. coli (SEQ ID NO:60). The sequences are the 23S rRNA from the following organisms: B. subtilis (SEQ ID NO:49); B. anthracis (SEQ ID NO. 50); E. facaelis (SEQ ID NO. 51); L. lactis (SEQ ID NO. 52); L. monocytogenes (SEQ ID NO. 53); S. aureus (SEQ ID NO. 54); S. mutans (SEQ ID NO. 55); S. pneumoniae (SEQ ID NO. 56); S. pyogenes (SEQ ID NO. 57); M. avium (SEQ ID NO. 58); M. tuberculosis (SEQ ID NO. 59); K. pneumoniae (SEQ ID NO. 61); H. influenzae (SEQ ID NO. 62); B. bronchiseptica (SEQ ID NO. 63); B. parapertussis (SEQ ID NO. 64); B. pertussis (SEQ ID NO. 65); B. cepacia (SEQ ID NO. 66); E. mallei (SEQ ID NO. 67); E. pseudomallei (SEQ ID NO. 68); N. gonorrhoeae (SEQ ID NO. 69); N. eminigititdis (SEQ ID NO. 70); P. aeruginosa (SEQ ID NO. 71); V. cholerae (SEQ ID NO. 72); Y. enterocolitica (SEQ ID NO. 73).

[0044]FIG. 3. Electropherograms of RNA from a control reaction. E. coli total RNA was purified with RNAwiz™ (Ambion) and carried through the rRNA depletion procedure as described in Example 2, except that bridging nucleic acids were left out of the reaction. A sample of the RNA was analyzed with the RNA 6000 Lab Chip Kit® (Caliper Technologies Corp.) using the Agilent 2100 Bioanalyzer (Agilent Technologies). The electropherogram shown was generated with Agilent 2100 Bioanalyzer Bio Sizing software (Version A.02.01).

[0045]FIG. 4. Electropherograms of RNA from an experimental reaction after ribosomal RNA depletion. E. coli total RNA was purified with RNAwiz™ (Ambion) and carried through the rRNA depletion procedure as described in Example 2. A sample of the RNA was analyzed as described in the legend to FIG. 3.

[0046] FIGS. 5A-B. Electropherograms of RNA from experiments. A. Agilent 2100 Bioanalyzer electropherogram of a sample from a control reaction performed as described in Example 5, but with no bridging oligonucleotides. The sample contains E. coli and rat liver total RNA. The RNA sample was analyzed with the RNA 6000 Lab Chip Kit® (Caliper Technologies Corp.) using the Agilent 2100 Bioanalyzer (Agilent Technologies). The electropherogram shown was generated with Agilent 2100 Bioanalyzer Bio Sizing software (Version A.02.01). B. Agilent 2100 Bioanalyzer electropherogram of a sample from an experimental reaction performed as described in Example 5 with bridging oligonucleotides. The sample is depleted of E. coli 16S and 23S rRNA and rat liver 18S and 28S rRNA. The RNA sample was analyzed with the RNA 6000 Lab Chip Kit® (Caliper Technologies Corp.) using the Agilent 2100 Bioanalyzer (Agilent Technologies). The electropherogram shown was generated with Agilent 2100 Bioanalyzer Bio Sizing software (Version A.02.01).

[0047] FIGS. 6A-B. Electropherograms of RNA from experiments. A. Agilent 2100 Bioanalyzer electropherogram of a sample from a control reaction performed as described in Example 6, but with no bridging oligonucleotides. The sample contains human liver total RNA. The RNA sample was analyzed with the RNA 6000 Lab Chip Kit® (Caliper Technologies Corp.) using the Agilent 2100 Bioanalyzer (Agilent Technologies). The electropherogram shown was generated with Agilent 2100 Bioanalyzer Bio Sizing software (Version A.02.01). B. Agilent 2100 Bioanalyzer electropherogram of a sample from an experimental reaction performed as described in Example 6 with bridging oligonucleotides. The sample is depleted of human 18S and 28S rRNA. The RNA sample was analyzed with the RNA 6000 Lab Chip Kit® (Caliper Technologies Corp.) using the Agilent 2100 Bioanalyzer (Agilent Technologies). The electropherogram shown was generated with Agilent 2100 Bioanalyzer Bio Sizing software (Version A.02.01).

[0048] FIGS. 7A-B. Electropherograms of RNA from experiments. A. Agilent 2100 Bioanalyzer electropherogram of a sample from a control reaction performed as described in Example 7, but with no bridging oligonucleotides. The sample contains rat liver total RNA. The RNA sample was analyzed with the RNA 6000 Lab Chip Kit® (Caliper Technologies Corp.) using the Agilent 2100 Bioanalyzer (Agilent Technologies). The electropherogram shown was generated with Agilent 2100 Bioanalyzer Bio Sizing software (Version A.02.01). B. Agilent 2100 Bioanalyzer electropherogram of a sample from an experimental reaction performed as described in Example 6 with bridging oligonucleotides. The sample is depleted of rat 18S and 28S rRNA. The RNA sample was analyzed with the RNA 6000 Lab Chip Kit® (Caliper Technologies Corp.) using the Agilent 2100 Bioanalyzer (Agilent Technologies). The electropherogram shown was generated with Agilent 2100 Bioanalyzer Bio Sizing software (Version A.02.01).

[0049] FIGS. 8A-B. Electropherograms of RNA from experiments. A. Agilent 2100 Bioanalyzer electropherogram of a sample from a control reaction performed as described in Example 6, but with no bridging oligonucleotides. The sample contains mouse liver total RNA. The RNA sample was analyzed with the RNA 6000 Lab Chip Kit® (Caliper Technologies Corp.) using the Agilent 2100 Bioanalyzer (Agilent Technologies). The electropherogram shown was generated with Agilent 2100 Bioanalyzer Bio Sizing software (Version A.02.01). B. Agilent 2100 Bioanalyzer electropherogram of a sample from an experimental reaction performed as described in Example 8 with bridging oligonucleotides. The sample is depleted of mouse 18S and 28S rRNA. The RNA sample was analyzed with the RNA 6000 Lab Chip Kite (Caliper Technologies Corp.) using the Agilent 2100 Bioanalyzer (Agilent Technologies). The electropherogram shown was generated with Agilent 2100 Bioanalyzer Bio Sizing software (Version A.02.01).

DESCRIPTION OF ILLUSTRATIVE EMBODIMENTS

[0050] The present invention concerns a system for isolating, depleting, or identifying specific, targeted nucleic acid populations, such as rRNA in a sample, in some cases for the purpose of enriching for other nucleic acid populations. The targeted nucleic acid, components of the system, and the methods for implementing the system, as well as variations thereof, are provided below.

[0051] I. Targeted Nucleic Acid

[0052] The present invention concerns targeting a particular nucleic acid population (i.e., mRNA, rRNA, tRNA, genomic DNA) or targeting types of a nucleic acid population, such as individual tRNAs, rRNAs (5S, 16S, or 23S rRNA from prokaryotes; 5.8S, 17S or 18S, or 28S from eukaryotes), or specific mRNAs. A nucleic acid is targeted by using a bridging nucleic acid that has a targeting region—a region complementary to all or part of the targeted nucleic acid.

[0053] In some embodiments, the invention is specifically concerned with depleting or isolating rRNA from other nucleic acids (“non-targeted nucleic acids” or “enriched population”). The 5S, 16S, and/or 23S rRNA from a prokaryote may be the targeted nucleic acid. Also, the 5.8S, 17S (observed in yeast) or 18S, and/or 28S from a eukaryote may be the targeted nucleic acid. Alternatively, rRNAs from both prokaryotes and eukaryotes may be targeted, such as with a sample that has eukaryotic host cells infected with a prokaryotic organism. The sequences for ribosomal RNAs are well known to those or ordinary skill in the art and can be readily found in sequence databases such as GenBank (www.ncbi.nlm.nih.gov/) or are published. Nucleic acids may be targeted by targeting regions that are complementary to all or part of the targeted nucleic acid. Targeted nucleic acids may be, be at least, or be at most 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 210, 220, 230, 240, 250, 260, 270, 280, 290, 300, 310, 320, 330, 340, 350, 360, 370, 380, 390, 400, 410, 420, 430, 440, 450, 460, 470, 480, 490, 500, 510, 520, 530, 540, 550, 560, 570, 580, 590, 600, 610, 620, 630, 640, 650, 660, 670, 680, 690, 700, 710, 720, 730, 740, 750, 760, 770, 780, 790, 800, 810, 820, 830, 840, 850, 860, 870, 880, 890, 900, 910, 920, 930, 940, 950, 960, 970, 980, 990, 1000, 1100, 1200, 1300, 1400, 1500, 1600, 1700, 1800, 1900, 2000, 2100, 2200, 2300, 2400, 2500, 2600, 2700, 2800, 2900, 3000, 3100, 3200, 3300, 3400, 3500, 3600, 3700, 3800, 3900, 4000, 4100, 4200, 4300, 4400, 4500, 4600, 4700, 4800, 4900, 5000, 5100, 5200, 5300, 5400, 5500, 5600, 5700, 5800, 5900, 6000, 6100, 6200, 6300, 6400, 6500, 6600, 6700, 6800, 6900, 7000, 7100, 7200, 7300, 7400, 7500, 7600, 7700, 7800, 7900, 8000, 8100, 8200, 8300, 8400, 8500, 8600, 8700, 8800, 8900, 9000, 9100, 9200, 9300, 9400, 9500, 9600, 9700, 9800, 9900, 10000, or more nucleotides in length. Furthermore, any region of at least five contiguous nucleotides in the targeted nucleic acid may be used as the targeted region-that is, the region that is complementary to the targeting region of a bridging nucleic acid. Also, there may be more than one targeted region in a targeted nucleic acid. There may be, be at least, or be at most 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more targeted regions in a targeted nucleic acid. A targeted region may be a region in a targeted nucleic acid that has greater than 70%, 80%, or 90% homology with a sequence from a different targeted nucleic acid. In some embodiments, the targeted region from a targeted nucleic acid is identical to a sequence in a different targeted nucleic acid. For example, 23S rRNA of various prokaryotes may be targeted using a targeted region common to a group of organisms, such as Gram negative bacteria or a subset of such bacteria. Alternatively, a targeted region may be a sequence unique to a particular targeted nucleic acid. However, for purposes of this application, a “targeted region” is not a poly-A region, such as a poly-A tail of an eukaryotic mRNA. Additional information regarding targeted rRNAs is provided below. This information is provided as an example of targeted nucleic acids. However, it is contemplated that there may be sequence variations from individual organism to organism and these sequences provided as simply an example of one sequenced nucleic acid, even though such variations exist in nature. It is contemplated that these variations may also be targeted, and this may or may not require changes to a targeting nucleic acid or to the hybridization conditions, depending on the variation, which one of ordinary skill in the art could evaluate and determine.

[0054] A number of patents concern a targeted nucleic acid, for example, U.S. Pat. Nos. 4,486,539; 4,563,419; 4,751,177; 4,868,105; 5,200,314; 5,273,882; 5,288,609; 5,457,025; 5,500,356; 5,589,335; 5,702,896; 5,714,324; 5,723,597; 5,759,777; 5,897,783; 6,013,440; 6,060,246; 6,090,548; 6,110,678; 6,203,978; 6,221,581; 6,228,580; and WO 01/32672, all of which are specifically incorporated herein by reference.

[0055] A. Prokaryotic rRNA

[0056] Prokaryotic rRNA can be a targeted nucleic acid of the invention. The following examples are provided, but the invention is not limited solely to these organisms and sequences (GenBank accession number provided and/or region within sequence that corresponds to the targeted rRNA): 1. Superkingdom Archaea (archaebacteria) Aeropyrum pernix 16S D83259 Aeropyrum pernix NC_000854 APErRNA05 (16S) 1218763-1220185 APErRNA03 (23S) 1213627-1218039 Methanococcus jannaschii 16S M59126 Methanococcus jannaschii NC_000909 MJrrnA16S 157985-159459 MJrrnA23S 154759-157648 Halobacterium marismortui 23S X13738 Halobacterium sp. NRC-1 NC_002607 rrs (16S) 1875505-1876977 rr1A (23S) 1877506-1880411 Thermoplasma acidophilum 23S M32298 Thermoplasma acidophilum NC_002578 16S 1475300-1475770 2. Superkingdom Eubacteria (eubacteria) a. Firmicutes (Gram-positive bacteria) i) Bacillus/Clostridium group (low G + C gram- positive bacteria) Listeria innocua Clip 11262 NC_003212 16S 260527-262081 23S 262327-265257 Listeria monocytogenes strain EGD NC_003210 16S 237466-239020 23S 239265-242195 Bacillus subtilis NC000964 RrnO 16S 9809-11361 RrnA 23S 11707-14634 Bacillus anthracis 16S (1508nt) AF155950 23S (2922nt) AF267877 Bacillus thuringiensis 16S (1486nt) D16281 23S (2923nt) AF267880 Staphylococcus aureus strain Mu50 NC_002758 16S 530479-532033 23S 532398-535231 Staphylococcus aureus N315 NC_002745 SarRNA01 16S 506138-507692 SarRNA02 23S 508166-510999 Clostridium acetobutylicum ATCC824 NC_003030 16SarRNA 9710-11219 23SarRNA 11398-14303 Clostridium difficile 16S (1470nt) X73450 Clostridium perfringens 16S M69264 (499-2294) Mycoplasma genitalium G37 L43967 MgrrnA16S 170009-171527 MgrrnA23S 171730-174463 Mycoplasma pneumoniae NC_000912 16S 118312-119824 23S 120057-122961 Mycoplasma pulmonis NC_002771 16S 813583-815113 23S 810563-813297 Streptococcus pneumoniae R6 NC_003098 RRNA16S-1 15161-16674 RRNA23S-1 16945-19846 Streptococcus pneumoniae TIGR4 AE005672 SprrnaA16S 15394-16806 SprrnaA23S 17142-20043 Streptococcus pyogenes AE004092 16S 17170-18504 23S 19037-21937 Streptococcus mutans 16S (1334nt) X58303 23S AF139599 (1940-4840) Lactococcus lactis 16S X64887 (508-2055) 23S X64887 (2360-5257) Enterococcus faecalis 16S (1449nt) Y18293 23S (2912nt) AJ295306 ii) Actinobacteria (high G + C gram-positive bacteria) Mycobacterium leprae strain TN NC_002677 Rrs16S 1341144-1342692 Rr123S 1342976-1346100 Mycobacterium tuberculosis CDC 1551 NC_002755 MtrrnaA16S 1471388-1472923 MtrrnaA23S 1473199-1476336 Mycobacterium avium 16S (1372nt) M61673 23S X74494 (295-3401) Corynebacterium glutamicum 16S (1479nt) Z46753 Rhodococcus equi 16S (1478nt) X80614 b. Spirochaetales (spirochetes) Borrelia burgdorferi AE000783 Rr1B 16S 444581-446118 Rr1B 23S 438590-441508 Treponema pallidum AE000520 TprrnaA16S 230162-231656 TprrnaA23S 231950-234850 Borrelia burgdorferi 16S AE001147 (9459-10996) 23S AE001147 (212-3145) c. Thermotogales Thermotoga maritima AE000512 TmrrnaA16S 188968-190526 TmrrnaA23S 190766-193787 d. Thermus/Deinococcus group Deinococcus radiodurans R1 NC_001263 DrrrnaA16S 2285518-2287019 DrrrnaA23S 2245319-2246194 Deinococcus radiodurans 16S AE002076 (7275-8776) 23S AE001886 (8829-10771) e. Chlamydiales (chlamydias) Chlamydia trachomatis AE001273 16SrRNA1 854128-855677 23SrRNA1 855993-858862 Chlamydophila pneumoniae AR39 NC_002179 CprrnA16S 1069329-1070785 CprrnA23S 1066159-1069022 Chlamydophila psittaci 16S U68447 (1-1553) 23S U68447 (1778-4721) f. Proteobacteria (purple bacteria) i) Alpha subdivision Rickettsia conorii Malish 7 NC_003103 Rrs16S 884601-886108 Rr123S 281797-284557 Rickettsia prowazekii strain Madrid E AJ235269 Rrs16S 772263-773769 Rr123S 257853-260613 Rickettsia typhi 16S (1444nt) M20499 23S Y13133 (956-3716) Ehrlichia bovis 16S (1488nt) U03775 Agrobacterium tumefaciens C58 AE007870 16S 768991-770427 23S 765313-767565 Brucella melitensis 16S AF220148 (645-2129) 23S AF220148 (2896-3024 . . . 3204-5807) Rhizobium rhizogenes 16S (1369nt) D13945 ii) Beta subdivision Neisseria meningitides strain MC58 AE002098 NmrrnaA16S 60971-62514 NmrrnaA23S 63178-66068 Bordetella bronchiseptica 16S (1532nt) X57026 23S (2865nt) X70371 Bordetella parapertussis 16S (1464nt) U04949 23S (2865nt) X68368 Bordetella pertussis 16S (1464nt) U04950 Burkholderi mallei 16S (1488nt) AF110188 23S (2882nt) Y17183 Burkholderi pseudomallei 16S (1488nt) U91839 23S (2882nt) Y17184 Neisseria gonorrhoeae 16S (1544nt) X07714 23S (2890nt) X67293 iii) Gamma group Buchnera sp. APS NC_002528 Rrs 16S 274065-275524 Rr1 23S 539539-542451 Escherichia coli K12 U00096 RrsH 16S 223771-225312 Rr1H 23S 225759-228662 Escherichia coli 0157:H7 NC_002695 RrsH 16S 227102-228643 Rr1H 23S 229090-231992 Salmonella enterica serovar Typhi NC_003198 16S 287479-289020 23S 289375-292380 Salmonella typhimurium LT2 NC_003197 RrsH 16S 289189-290732 RrlH 23S 291244-294336 Yersinia pestis NC_003143 16S 12292-13763 23S 14272-17178 Klebsiella pneumoniae 16S (1534nt) X87276 23S (2903nt) X87284 Yersinia enterocolitica 16S (1484nt) Z49830 23S (2906nt) U77925 Proteus vulgaris 16S (2067nt) X07652 Shigella flexneri 16S (1468nt) X80679 Shigella sonnei 16S (1467nt) X80726 Shigella dysenterica 16S (1487nt) X96966 Haemophilus influenzae Rd L42023 HirrnE16S 1511137-1512634 HirrnE23S 123801-126697 Pasteurella multocida 16S (1543nt) M35018 Actinobacillus actinomycetemcomitans 16S (1485nt) M75037 Actinobacillus pleuropneumoniae 16S D30032 (83-1625) Haemophilus somnus 16S (1483nt) M75046 Legionella pneumophila 16S (1544nt) M59157 Mannheimia haemolytica 16S (1472nt) U57072 Vibrio cholerae chromosomel NC_002505 16Sa rRNA 53823-55357 23Sa rRNA 55784-58670 Vibrio parahaemolyticus 16S (1499nt) M59161 Coxiella burnetii 16S (1484nt) M21291 23S X79704 (1620-3350) Aeromonas hydrophila 16S (1538nt) X87271 Aeromonas salmonicida 16S (1502nt) X60405 Francisella tularesis 16S (1517nt) Z21931 Moraxella catarrhalis 16S (1511nt) U10876 Pseudomonas aeruginosa AE004091 16S 722096-726631 23S 724103-726993 Pseudomonas putida 16S (1527nt) D84020 iv) Delta/Epsilon subdivisions Campylobacter jejuni AL111168 16S 39249-40761 23S 41568-44457 Helicobacter pylori 26695 NC_000915 HPrrnB16S 1511137-1512634 HPrrnB23S 1473918-1476893 g. Cyanobacteria Synechocystis sp. PCC 6803 NC_000911 Rrn16Sa 2452187-2453675 Rrn23Sa 2448839-2451721 Synechococcus sp. (Anacystis nidulans) 16S X03538 (1432-2918) 23S X00512 (251-3126) h. CFB/Green sulfer bacteria group Porphyromonas gingivalis 16S (1474nt) L16492

[0057] B. Eukaryotic rRNA

[0058] Targeted nucleic acids of the invention may also be one or more types of eukaryotic rRNAs. Eukaryotes include, but are not limited to: mammals, fish, birds, amphibians, fungi, and plants. The following provides sequences for some of these targeted nucleic acids. It is contemplated that other eukaryotic rRNA sequences can be readily obtained by one of ordinary skill in the art, and thus, the invention includes, but is not limited to, the sequences shown below. Superkingdom Eukaryota (eucaryotes) Homo sapiens (human) 18S M10098 18S K03432 18S X03205 28S M11167 Mus muculus 18S X00686 28S X00525 Rattus norvegicus 18S M11188 18S X01117 Rattus norvegicus V01270.1 18S 1-1874 28S 3862-8647

[0059] II. Isolation and/or Depletion System Nucleic Acids

[0060] The present invention concerns compositions comprising a nucleic acid or a nucleic acid analog in a system or kit to deplete, isolate, or separate a nucleic acid population from other nucleic acid populations, for which enrichment may be desirable. It concerns a bridging nucleic acid and a capture nucleic acid to deplete, isolate, or separate out a targeted nucleic acid, as discussed above.

[0061] A. Bridging Nucleic Acids

[0062] Bridging nucleic acids of the invention comprise a bridging region and a targeting region. As discussed in other sections, the location of these regions may be throughout the molecule, which may be of a variety of lengths. The bridging nucleic acid may comprise RNA, DNA, both, or analogs of either or both.

[0063] The bridging region comprises a sequence that is complementary to at least five contiguous nucleotides in the capture nucleic acid. It is contemplated that that this region may be a homogenous sequence, that is, have the same nucleotide repeated across its length, such as a repeat of A, C, G, T, or U residues. However, to avoid hybridizing with a poly-A tailed mRNA in a sample comprising eukaryotic nucleic acids, it is contemplated that most embodiments will not have a poly-U or poly-T bridging region when dealing with such samples having poly-A tailed RNA. In some embodiments, the bridging region is a poly-C region and the capture region is a poly-G region, or vice versa. In other embodiments, the bridging region will be a random sequence that is complementary to the capture region (or the capture region will be random and the bridging region will be complementary to it). In further embodiments, the bridging region will have a designed sequence that is not homopolymeric but that is complementary to the capture region or vice versa. Sequences may be determined empirically. In many embodiments, it is preferred that this will be a random sequence or a defined sequence that is not a homopolymer. Some sequences will be determined empirically during evaluation in the assay.

[0064] B. Capture Nucleic Acids

[0065] Capture nucleic acids of the invention comprise a capture region and a nonreacting structure that allows the capture nucleic acid, any molecules specifically binding or hybridizing to the capture nucleic acid—such as the bridging nucleic acid—and any molecules specifically binding or hybridizing to the bridging nucleic acid—such as the targeted nucleic acid—to be isolated away from other nucleic acid populations.

[0066] The capture nucleic acid may comprise RNA, DNA, both, or analogs of either or both. However, in some embodiments of the invention, it is specifically contemplated to be homopolymeric (only one type of nucleotide residue in molecule, such as poly-C), though in other embodiments, it is specifically contemplated not to be homopolymeric and be heteropolymeric, as described for bridging regions.

[0067] 1. Capture Regions

[0068] The main requirement for bridging and capture nucleic acid sequences is that they are complementary to one another. The capture region may be a poly-pyrimidine or poly-purine region comprising at least 5 nucleic acid residues. In addition, it may be heteropolymeric, either a random sequence or a designed sequence that is complementary to the bridging region of the nucleic acid with which it should hybridize.

[0069] 2. Nonreacting Structures

[0070] A nonreacting structure is a compound or structure that will not react chemically with nucleic acids, and in some embodiments, with any molecule that may be in a sample. Nonreacting structures may comprise plastic, glass, teflon, silica, a magnet, a metal such as gold, carbon, cellulose, latex, polystyrene, and other synthetic polymers, nylon, cellulose, nitrocellulose, polymethacrylate, polyvinylchloride, styrene-divinylbenzene, or any chemically-modified plastic. They may also be porous or non-porous materials. The structure may also be a particle of any shape that allows the targeted nucleic acid to be isolated, depleted, or separated. It may be a sphere, such as a bead, or a rod, or a flat-shaped structure, such as a plate with wells. Also, it is contemplated that the structure may be isolated by physical means or electromagnetic means. For example, a magnetic field may be used to attract a non-reacting structure that includes a magnet. The magnetic field may be in a stand or it may simply be placed on the side of a tube with the sample and a capture nucleic acid that is magnetized. Examples of physical ways to separate nucleic acids with their specifically hybridizing compounds are well known to those of skill in the art. A basket or other filter means may be employed to separate the capture nucleic acid and its hybridizing compounds (direct and indirect). The non-reacting structure and sample with nucleic acids of the invention may be centrifuged, filtered, dialyzed, or captured (with a magnet). When the structure is centrifuged it may be pelleted or passed through a centrifugible filter apparatus. The structure may also be filtered, including filtration using a pressure-driven system. Many such structures are available commercially and may be utilized herewith. Other examples can be found in WO 86/05815, WO90/06045, U.S. Pat. No. 5,945,525, all of which are specifically incorporated by reference.

[0071] Cellulose is a structural polymer derived from vascular plants. Chemically, it is a linear polymer of the monosaccharide glucose, using β, 1-4 linkages. Cellulose can be provided commercially, including from the Whatman company, and can be chemically sheared or chemically modified to create preparations of a more fibrous or particulate nature. CF-1 cellulose from Whatman is an example that can be implemented in the present invention.

[0072] Synthetic plastic or glass beads may be employed in the context of the invention. The beads may be complexed with avidin or streptavidin and they may also be magnetized. The complexed streptavidin can be used to capture biotin linked to an oligo-dT or -U or poly (dT) or poly(U) moiety, either before or after hybridization to the poly(A) tails of mRNA. Alternatively, the oligo/poly(dT/U) moiety can be attached to the beads directly through chemical coupling. The beads may be collected using gravity- or pressure-based systems and/or filtration devices. If the beads are magnetized, a magnet can be used to separate the beads from the rest of the sample. The magnet may be employed with a stand or a stick or other type of physical structure to facilitate isolation.

[0073] Other components include isolation apparatuses such as filtration devices, including spin filters or spin columns.

[0074] C. Nucleic Acid Compositions

[0075] Embodiments of the present invention concern bridging, capture, and targeted nucleic acids. In particular aspects, a targeted nucleic acid encodes for or comprises a transcribed nucleic acid. In other aspects, a bridging nucleic acid comprises a targeting region that comprises a nucleic acid segment having the sequence of all or part of SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO: 8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12, SEQ ID NO:13, SEQ ID NO:14, SEQ ID NO:15, SEQ ID NO:16, SEQ ID NO:17, SEQ ID NO:18, SEQ ID NO:19, SEQ ID NO:20, SEQ ID NO:21, SEQ ID NO:22, SEQ ID NO:23, SEQ ID NO:24, SEQ ID NO:25, SEQ ID NO:26, SEQ ID NO:27, SEQ ID NO:28, SEQ ID NO:29, SEQ ID NO:30, SEQ ID NO:31, SEQ ID NO:32, SEQ ID NO:33, SEQ ID NO:34, SEQ ID NO:35, SEQ ID NO:36, SEQ ID NO:37, SEQ ID NO:38, SEQ ID NO:39, SEQ ID NO:40, SEQ ID NO:41, SEQ ID NO:42, SEQ ID NO:43, SEQ ID NO:44, SEQ ID NO:45, SEQ ID NO:46, SEQ ID NO:47, SEQ ID NO:48, SEQ ID NO:49, SEQ ID NO:50, SEQ ID NO:51, SEQ ID NO:52, SEQ ID NO:53, SEQ ID NO:54, SEQ ID NO:55, SEQ ID NO:56, SEQ ID NO:57, SEQ ID NO:58, SEQ ID NO:59, SEQ ID NO:60, SEQ ID NO:61, SEQ ID NO:62, SEQ ID NO:63, SEQ ID NO:64, SEQ ID NO:65, SEQ ID NO:66, SEQ ID NO:67, SEQ ID NO:68, SEQ ID NO:69, SEQ ID NO:71, SEQ ID NO:72, or SEQ ID NO:73 (collectively referred to as “SEQ ID NOS:1-73”). In particular aspects, a targeted nucleic acid encodes a protein, polypeptide, peptide. Nucleic acids of the invention comprise RNA, DNA, analogs of RNA, analogs of DNA, or a combination thereof.

[0076] The term “nucleic acid” is well known in the art. A “nucleic acid” as used herein will generally refer to a molecule (i.e., a strand) of DNA, RNA or a derivative or analog thereof, comprising a nucleobase. A nucleobase includes, for example, a naturally occurring purine or pyrimidine base found in DNA (e.g., an adenine “A,” a guanine “G,” a thymine “T” or a cytosine “C”) or RNA (e.g., an A, a G, an uracil “U” or a C). The term “nucleic acid” encompass the terms “oligonucleotide” and “polynucleotide,” each as a subgenus of the term “nucleic acid.” The term “oligonucleotide” refers to a molecule of between about 3 and about 100 nucleobases in length. The term “polynucleotide” refers to at least one molecule of greater than about 100 nucleobases in length.

[0077] These definitions generally refer to a single-stranded molecule, but in specific embodiments will also encompass an additional strand that is partially, substantially or fully complementary to the single-stranded molecule. Thus, a nucleic acid may encompass a double-stranded molecule or a triple-stranded molecule that comprises one or more complementary strand(s) or “complement(s)” of a particular sequence comprising a molecule. As used herein, a single stranded nucleic acid may be denoted by the prefix “ss,” a double stranded nucleic acid by the prefix “ds,” and a triple stranded nucleic acid by the prefix “ts.”

[0078] 1. Nucleobases

[0079] As used herein a “nucleobase” refers to a heterocyclic base, such as for example a naturally occurring nucleobase (i.e., an A, T, G, C or U) found in at least one naturally occurring nucleic acid (i.e., DNA and RNA), and naturally or non-naturally occurring derivative(s) and analogs of such a nucleobase. A nucleobase generally can form one or more hydrogen bonds (“anneal” or “hybridize”) with at least one naturally occurring nucleobase in manner that may substitute for naturally occurring nucleobase pairing (e.g., the hydrogen bonding between A and T, G and C, and A and U).

[0080] “Purine” and/or “pyrimidine” nucleobase(s) encompass naturally occurring purine and/or pyrimidine nucleobases and also derivative(s) and analog(s) thereof, including but not limited to, those of a purine or pyrimidine substituted by one or more of an alkyl, caboxyalkyl, amino, hydroxyl, halogen (i.e., fluoro, chloro, bromo, or iodo), thiol or alkylthiol moiety. Preferred alkyl (e.g., alkyl, caboxyalkyl, etc.) moieties comprise of from about 1, about 2, about 3, about 4, about 5, to about 6 carbon atoms. Other non-limiting examples of a purine or pyrimidine include a deazapurine, a 2,6-diaminopurine, a 5-fluorouracil, a xanthine, a hypoxanthine, a 8-bromoguanine, a 8-chloroguanine, a bromothymine, a 8-aminoguanine, a 8-hydroxyguanine, a 8-methylguanine, a 8-thioguanine, an azaguanine, a 2-aminopurine, a 5-ethylcytosine, a 5-methylcyosine, a 5-bromouracil, a 5-ethyluracil, a 5-iodouracil, a 5-chlorouracil, a 5-propyluracil, a thiouracil, a 2-methyladenine, a methylthioadenine, a N,N-diemethyladenine, an azaadenines, a 8-bromoadenine, a 8-hydroxyadenine, a 6-hydroxyaminopurine, a 6-thiopurine, a 4-(6-aminohexyl/cytosine), and the like. A table of non-limiting, purine and pyrimidine derivatives and analogs is also provided herein below. TABLE 1 Purine and Pyrimidine Derivatives or Analogs Abbr. Modified base description ac4c 4-acetylcytidine Chm5u 5-(carboxyhydroxylmethyl) uridine Cm 2′-O-methylcytidine Cmnm5s2u 5-carboxymethylamino-methyl-2- thioridine Cmnm5u 5-carboxymethylaminomethyluridine D Dihydrouridine Fm 2′-O-methylpseudouridine Gal q Beta,D-galactosylqueosine Gm 2′-O-methylguanosine I Inosine I6a N6-isopentenyladenosine m1a 1-methyladenosine m1f 1-methylpseudouridine m1g 1-methylguanosine m1I 1-methylinosine m22g 2,2-dimethylguanosine m2a 2-methyladenosine m2g 2-methylguanosine m3c 3-methylcytidine m5c 5-methylcytidine m6a N6-methyladenosine m7g 7-methylguanosine Mam5u 5-methylaminomethyluridine Mam5s2u 5-methoxyaminomethyl-2-thiouridine Man q Beta,D-mannosylqueosine Mcm5s2u 5-methoxycarbonylmethyl-2-thiouridine Mcm5u 5-methoxycarbonylmethyluridine Mo5u 5-methoxyuridine Ms2i6a 2-methylthio-N6-isopentenyladenosine Ms2t6a N-((9-beta-D-ribofuranosyl-2- methylthiopurine-6-yl)carbamoyl)threonine Mt6a N-((9-beta-D-ribofuranosylpurine-6-yl)N- methyl-carbamoyl)threonine Mv Uridine-5-oxyacetic acid methylester o5u Uridine-5-oxyacetic acid (v) Osyw Wybutoxosine P Pseudouridine Q Queosine s2c 2-thiocytidine s2t 5-methyl-2-thiouridine s2u 2-thiouridine s4u 4-thiouridine T 5-methyluridine t6a N-((9-beta-D-ribofuranosylpurine-6- yl)carbamoyl)threonine Tm 2′-O-methyl-5-methyluridine Um 2′-O-methyluridine Yw Wybutosine X 3-(3-amino-3-carboxypropyl)uridine, (acp3)u

[0081] A nucleobase may be comprised of a nucleoside or nucleotide, using any chemical or natural synthesis method described herein or known to one of ordinary skill in the art.

[0082] 2. Nucleosides

[0083] As used herein, a “nucleoside” refers to an individual chemical unit comprising a nucleobase covalently attached to a nucleobase linker moiety. A non-limiting example of a “nucleobase linker moiety” is a sugar comprising 5-carbon atoms (i.e., a “5-carbon sugar”), including but not limited to a deoxyribose, a ribose, an arabinose, or a derivative or an analog of a 5-carbon sugar. Non-limiting examples of a derivative or an analog of a 5-carbon sugar include a 2′-fluoro-2′-deoxyribose or a carbocyclic sugar where a carbon is substituted for an oxygen atom in the sugar ring.

[0084] Different types of covalent attachment(s) of a nucleobase to a nucleobase linker moiety are known in the art. By way of non-limiting example, a nucleoside comprising a purine (i.e., A or G) or a 7-deazapurine nucleobase typically covalently attaches the 9 position of a purine or a 7-deazapurine to the 1′-position of a 5-carbon sugar. In another non-limiting example, a nucleoside comprising a pyrimidine nucleobase (i e., C, T or U) typically covalently attaches a 1 position of a pyrimidine to a 1′-position of a 5-carbon sugar.

[0085] 3. Nucleotides

[0086] As used herein, a “nucleotide” refers to a nucleoside further comprising a “backbone moiety”. A backbone moiety generally covalently attaches a nucleotide to another molecule comprising a nucleotide, or to another nucleotide to form a nucleic acid. The “backbone moiety” in naturally occurring nucleotides typically comprises a phosphorus moiety, which is covalently attached to a 5-carbon sugar. The attachment of the backbone moiety typically occurs at either the 3′- or 5′-position of the 5-carbon sugar. However, other types of attachments are known in the art, particularly when a nucleotide comprises derivatives or analogs of a naturally occurring 5-carbon sugar or phosphorus moiety.

[0087] 4. Nucleic Acid Analogs

[0088] A nucleic acid may comprise, or be composed entirely of, a derivative or analog of a nucleobase, a nucleobase linker moiety and/or backbone moiety that may be present in a naturally occurring nucleic acid. As used herein a “derivative” refers to a chemically modified or altered form of a naturally occurring molecule, while the terms “mimic” or “analog” refer to a molecule that may or may not structurally resemble a naturally occurring molecule or moiety, but possesses similar functions. As used herein, a “moiety” generally refers to a smaller chemical or molecular component of a larger chemical or molecular structure. Nucleobase, nucleoside and nucleotide analogs or derivatives are well known in the art, and have been described (see for example, Scheit, 1980, incorporated herein by reference).

[0089] Additional non-limiting examples of nucleosides, nucleotides or nucleic acids comprising 5-carbon sugar and/or backbone moiety derivatives or analogs, include those in U.S. Pat. No. 5,681,947 which describes oligonucleotides comprising purine derivatives that form triple helixes with and/or prevent expression of dsDNA; U.S. Pat. Nos. 5,652,099 and 5,763,167 which describe nucleic acids incorporating fluorescent analogs of nucleosides found in DNA or RNA, particularly for use as fluorescent nucleic acids probes; U.S. Pat. No. 5,614,617 which describes oligonucleotide analogs with substitutions on pyrimidine rings that possess enhanced nuclease stability; U.S. Pat. Nos. 5,670,663, 5,872,232 and 5,859,221 which describe oligonucleotide analogs with modified 5-carbon sugars (i.e., modified 2′-deoxyfuranosyl moieties) used in nucleic acid detection; U.S. Pat. No. 5,446,137 which describes oligonucleotides comprising at least one 5-carbon sugar moiety substituted at the 4′ position with a substituent other than hydrogen that can be used in hybridization assays; U.S. Pat. No. 5,886,165 which describes oligonucleotides with both deoxyribonucleotides with 3′-5′ internucleotide linkages and ribonucleotides with 2′-5′ internucleotide linkages; U.S. Pat. No. 5,714,606 which describes a modified internucleotide linkage wherein a 3′-position oxygen of the internucleotide linkage is replaced by a carbon to enhance the nuclease resistance of nucleic acids; U.S. Pat. No. 5,672,697 which describes oligonucleotides containing one or more 5′ methylene phosphonate internucleotide linkages that enhance nuclease resistance; U.S. Pat. Nos. 5,466,786 and 5,792,847 which describe the linkage of a substituent moiety, which may comprise a drug or label to the 2′ carbon of an oligonucleotide to provide enhanced nuclease stability and ability to deliver drugs or detection moieties; U.S. Pat. No. 5,223,618 which describes oligonucleotide analogs with a 2 or 3 carbon backbone linkage attaching the 4′ position and 3′ position of adjacent 5-carbon sugar moiety to enhanced cellular uptake, resistance to nucleases and hybridization to target RNA; U.S. Pat. No. 5,470,967 which describes oligonucleotides comprising at least one sulfamate or sulfamide internucleotide linkage that are useful as nucleic acid hybridization probe; U.S. Pat. Nos. 5,378,825, 5,777,092, 5,623,070, 5,610,289 and 5,602,240 which describe oligonucleotides with three or four atom linker moiety replacing phosphodiester backbone moiety used for improved nuclease resistance, cellular uptake and regulating RNA expression; U.S. Pat. No. 5,858,988 which describes hydrophobic carrier agent attached to the 2′-O position of oligonucleotides to enhanced their membrane permeability and stability; U.S. Pat. No. 5,214,136, which describes oligonucleotides conjugated to anthraquinone at the 5′ terminus that possess enhanced hybridization to DNA or RNA; enhanced stability to nucleases; U.S. Pat. No. 5,700,922 which describes PNA-DNA-PNA chimeras wherein the DNA comprises 2′-deoxy-erythro-pentofuranosyl nucleotides for enhanced nuclease resistance, binding affinity, and ability to activate RNase H; and U.S. Pat. No. 5,708,154 which describes RNA linked to a DNA to form a DNA-RNA hybrid. Other analogs that may be used with compositions of the invention include U.S. Pat. No. 5,216,141 (discussing oligonucleotide analogs containing sulfur linkages), U.S. Pat. No. 5,432,272 (concerning oligonucleotides having nucleotides with heterocyclic bases), and U.S. Pat. Nos. 6,001,983, 6,037,120, 6,140,496 (involving oligonucleotides with non-standard bases), all of which are incorporated by reference.

[0090] 5. Polyether and Peptide Nucleic Acids and Locked Nucleic Acids

[0091] In certain embodiments, it is contemplated that a nucleic acid comprising a derivative or analog of a nucleoside or nucleotide may be used in the methods and compositions of the invention. A non-limiting example is a “polyether nucleic acid”, described in U.S. Pat. No. 5,908,845, incorporated herein by reference. In a polyether nucleic acid, one or more nucleobases are linked to chiral carbon atoms in a polyether backbone.

[0092] Another non-limiting example is a “peptide nucleic acid”, also known as a “PNA”, “peptide-based nucleic acid analog” or “PENAM”, described in U.S. Pat. Nos. 5,786,461, 5,891,625, 5,773,571, 5,766,855, 5,736,336, 5,719,262, 5,714,331, 5,539,082, and WO 92/20702, each of which is incorporated herein by reference. Peptide nucleic acids generally have enhanced sequence specificity, binding properties, and resistance to enzymatic degradation in comparison to molecules such as DNA and RNA (Egholm et al., 1993; PCT/EP/01219). A peptide nucleic acid generally comprises one or more nucleotides or nucleosides that comprise a nucleobase moiety, a nucleobase linker moiety that is not a 5-carbon sugar, and/or a backbone moiety that is not a phosphate backbone moiety. Examples of nucleobase linker moieties described for PNAs include aza nitrogen atoms, amido and/or ureido tethers (see for example, U.S. Pat. No. 5,539,082). Examples of backbone moieties described for PNAs include an aminoethylglycine, polyamide, polyethyl, polythioamide, polysulfinamide or polysulfonamide backbone moiety.

[0093] In certain embodiments, a nucleic acid analogue such as a peptide nucleic acid may be used to inhibit nucleic acid amplification, such as in PCR, to reduce false positives and discriminate between single base mutants, as described in U.S. Pat. No. 5,891,625. Other modifications and uses of nucleic acid analogs are known in the art, and are encompassed by the bridging and capture nucleic acids of the invention. In a non-limiting example, U.S. Pat. No. 5,786,461 describes PNAs with amino acid side chains attached to the PNA backbone to enhance solubility of the molecule. In another example, the cellular uptake property of PNAs is increased by attachment of a lipophilic group. Several alkylamino moieties used to enhance cellular uptake of a PNA are described in U.S. Pat. Nos. 5,766,855, 5,719,262, 5,714,331 and 5,736,336, which describe PNAs comprising naturally and non-naturally occurring nucleobases and alkylamine side chains that provide improvements in sequence specificity, solubility and/or binding affinity relative to a naturally occurring nucleic acid.

[0094] Another non-limiting example is a locked nucleic acid or “LNA.” An LNA monomer is a bicyclic compound that is structurally similar to RNA nucleosides. LNAs have a furanose conformation that is restricted by a methylene linker that connects the 2′-O position to the 4′-C position, as described in Koshkin et al, 1998a and 1998b and Wahlestedt et al., 2000.

[0095] 6. Preparation of Nucleic Acids

[0096] A nucleic acid may be made by any technique known to one of ordinary skill in the art, such as for example, chemical synthesis, enzymatic production or biological production. Non-limiting examples of a synthetic nucleic acid (e.g., a synthetic oligonucleotide), include a nucleic acid made by in vitro chemical synthesis using phosphotriester, phosphite or phosphoramidite chemistry and solid phase techniques such as described in EP 266,032, incorporated herein by reference, or via deoxynucleoside H-phosphonate intermediates as described by Froehler et al., 1986 and U.S. Pat. No. 5,705,629, each incorporated herein by reference. In the methods of the present invention, one or more oligonucleotide may be used. Various different mechanisms of oligonucleotide synthesis have been disclosed in for example, U.S. Pat. Nos. 4,659,774, 4,816,571, 5,141,813, 5,264,566, 4,959,463, 5,428,148, 5,554,744, 5,574,146, 5,602,244, each of which is incorporated herein by reference.

[0097] A non-limiting example of an enzymatically produced nucleic acid include one produced by enzymes in amplification reactions such as PCR™ (see for example, U.S. Pat. No. 4,683,202 and U.S. Pat. No. 4,682,195, each incorporated herein by reference), or the synthesis of an oligonucleotide described in U.S. Pat. No. 5,645,897, incorporated herein by reference. A non-limiting example of a biologically produced nucleic acid includes a recombinant nucleic acid produced (i.e., replicated) in a living cell, such as a recombinant DNA vector replicated in bacteria (see for example, Sambrook et al. 1989, incorporated herein by reference).

[0098] 7. Purification of Nucleic Acids

[0099] A nucleic acid may be purified on polyacrylamide gels, cesium chloride centrifugation gradients, or by any other means known to one of ordinary skill in the art (see for example, Sambrook et al., 1989, incorporated herein by reference).

[0100] In certain aspect, the present invention concerns a nucleic acid that is an isolated nucleic acid. As used herein, the term “isolated nucleic acid” refers to a nucleic acid molecule (e.g., an RNA or DNA molecule) that has been isolated free of, or is otherwise free of, the bulk of the total genomic and transcribed nucleic acids of one or more cells. In certain embodiments, “isolated nucleic acid” refers to a nucleic acid that has been isolated free of, or is otherwise free of, bulk of cellular components or in vitro reaction components such as for example, macromolecules such as lipids or proteins, small biological molecules, and the like.

[0101] 8. Nucleic Acid Segments

[0102] In certain embodiments, the nucleic acid comprises a nucleic acid segment. As used herein, the term “nucleic acid segment,” are smaller fragments of a nucleic acid, such as for non-limiting example, those that correspond to targeted, targeting, bridging, and capture regions. Thus, a “nucleic acid segment” may comprise any part of a gene sequence, of from about 2 nucleotides to the full length of a targeted nucleic acid, capture nucleic acid, or bridging nucleic acid.

[0103] Various nucleic acid segments may be designed based on a particular nucleic acid sequence, and may be of any length. By assigning numeric values to a sequence, for example, the first residue is 1, the second residue is 2, etc., an algorithm defining all nucleic acid segments can be created:

n to n+y

[0104] where n is an integer from 1 to the last number of the sequence and y is the length of the nucleic acid segment minus one, where n+y does not exceed the last number of the sequence. Thus, for a 10-mer, the nucleic acid segments correspond to bases 1 to 10, 2 to 11, 3 to 12 . . . and so on. For a 15-mer, the nucleic acid segments correspond to bases 1 to 15, 2 to 16, 3 to 17 . . . and so on. For a 20-mer, the nucleic segments correspond to bases 1 to 20, 2 to 21, 3 to 22 . . . and so on. In certain embodiments, the nucleic acid segment may be a probe or primer. As used herein, a “probe” generally refers to a nucleic acid used in a detection method or composition. As used herein, a “primer” generally refers to a nucleic acid used in an extension or amplification method or composition.

[0105] 9. Nucleic Acid Complements

[0106] The present invention also encompasses a nucleic acid that is complementary to a other nucleic acids of the invention and targeted nucleic acids. More specifically, a targeting region in a bridging nucleic acid is complementary to the targeted region of the targeted nucleic acid and a bridging region of the bridging nucleic acid is complementary to a capture region of a capture nucleic acid. In particular embodiments the invention encompasses a nucleic acid or a nucleic acid segment identical or complementary to all or part of the sequences set forth in SEQ ID NOS: 1-73. A nucleic acid is “complement(s)” or is “complementary” to another nucleic acid when it is capable of base-pairing with another nucleic acid according to the standard Watson-Crick, Hoogsteen or reverse Hoogsteen binding complementarity rules. Unless otherwise specified, a nucleic acid region is “complementary” to another nucleic acid region if there is at least 70, 80%, 90% or 100% Watson-Crick base-pairing (A:T or A:U, C:G) between or between at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 210, 220, 230, 240, 250, 260, 270, 280, 290, 300, 310, 320, 330, 340, 350, 360, 370, 380, 390, 400, 410, 420, 430, 440, 450, 460, 470, 480, 490, 500 or more contiguous nucleic acid bases of the regions. As used herein “another nucleic acid” may refer to a separate molecule or a spatial separated sequence of the same molecule.

[0107] As used herein, the term “complementary” or “complement(s)” also refers to a nucleic acid comprising a sequence of consecutive nucleobases or semiconsecutive nucleobases (e.g., one or more nucleobase moieties are not present in the molecule) capable of hybridizing to another nucleic acid strand or duplex even if less than all the nucleobases do not base pair with a counterpart nucleobase. In certain embodiments, a “complementary” nucleic acid comprises a sequence in which at least 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100%, and any range derivable therein, of the nucleobase sequence is capable of base-pairing with a single or double stranded nucleic acid molecule during hybridization, as described in the Examples. In certain embodiments, the term “complementary” refers to a nucleic acid that may hybridize to another nucleic acid strand or duplex under conditions described in the Examples, as would be understood by one of ordinary skill in the art.

[0108] In certain embodiments, a “partly complementary” nucleic acid comprises a sequence that may hybridize in low stringency conditions to a single or double stranded nucleic acid, or contains a sequence in which less than about 70% of the nucleobase sequence is capable of base-pairing with a single or double stranded nucleic acid molecule during hybridization.

[0109] 10. Hybridization

[0110] As used herein, “hybridization”, “hybridizes” or “capable of hybridizing” is understood to mean the forming of a double or triple stranded molecule or a molecule with partial double or triple stranded nature. The term “anneal” as used herein is synonymous with “hybridize.” The term “hybridization”, “hybridize(s)” or “capable of hybridizing” encompasses the terms “stringent condition(s)” or “high stringency” and the terms “low stringency” or “low stringency condition(s).”

[0111] As used herein “stringent condition(s)” or “high stringency” are those conditions that allow hybridization between or within one or more nucleic acid strand(s) containing complementary sequence(s), but precludes hybridization of random sequences. Stringent conditions tolerate little, if any, mismatch between a nucleic acid and a target strand. Such conditions are well known to those of ordinary skill in the art, and are preferred for applications requiring high selectivity. Non-limiting applications include isolating a nucleic acid, such as a gene or a nucleic acid segment thereof, or detecting at least one specific mRNA transcript or a nucleic acid segment thereof, and the like.

[0112] Stringent conditions may comprise low salt and/or high temperature conditions, such as provided by about 0.02 M to about 0.15 M NaCl at temperatures of about 50° C. to about 70° C. Alternatively, stringent conditions may be determined largely by temperature in the presence of a TMAC solution with a defined molarity such as 3M TMAC. For example, in 3 M TMAC, stringent conditions include the following: for complementary nucleic acids with a length of 15 bp, a temperature of 45° C. to 55° C.; for complementary nucleotides with a length of 27 bases, a temperature of 65° C. to 75° C.; and, for complementary nucleotides with a length of >200 nucleotides, a temperature of 90° C. to 95° C. The publication of Wood et al., 1985, which is specifically incorporated by reference, provides examples of these parameters. It is understood that the temperature and ionic strength of a desired stringency are determined in part by the length of the particular nucleic acid(s), the length and nucleobase content of the target sequence(s), the charge composition of the nucleic acid(s), and to the presence or concentration of formamide, tetramethylammonium chloride or other solvent(s) in a hybridization mixture.

[0113] It is also understood that these ranges, compositions and conditions for hybridization are mentioned by way of non-limiting examples only, and that the desired stringency for a particular hybridization reaction is often determined empirically by comparison to one or more positive or negative controls. Depending on the application envisioned it is preferred to employ varying conditions of hybridization to achieve varying degrees of selectivity of a nucleic acid towards a target sequence. In a non-limiting example, identification or isolation of a related target nucleic acid that does not hybridize to a nucleic acid under stringent conditions may be achieved by hybridization at low temperature and/or high ionic strength. Such conditions are termed “low stringency” or “low stringency conditions”, and non-limiting examples of low stringency include hybridization performed at about 0.15 M to about 0.9 M NaCl at a temperature range of about 20° C. to about 50° C. Of course, it is within the skill of one in the art to further modify the low or high stringency conditions to suite a particular application.

[0114] 11. Oligonucleotide Synthesis

[0115] Oligonucleotide synthesis is performed according to standard methods. See, for example, Itakura and Riggs (1980). Additionally, U.S. Pat. No. 4,704,362; U.S. Pat. No. 5,221,619, U.S. Pat. No. 5,583,013 each describe various methods of preparing synthetic structural genes.

[0116] Oligonucleotide synthesis is well known to those of skill in the art. Various different mechanisms of oligonucleotide synthesis have been disclosed in for example, U.S. Pat. Nos. 4,659,774, 4,816,571, 5,141,813, 5,264,566, 4,959,463, 5,428,148, 5,554,744, 5,574,146, 5,602,244, each of which is incorporated herein by reference.

[0117] Basically, chemical synthesis can be achieved by the diester method, the triester method polynucleotides phosphorylase method and by solid-phase chemistry. These methods are discussed in further detail below.

[0118] Diester method. The diester method was the first to be developed to a usable state, primarily by Khorana and co-workers. (Khorana, 1979). The basic step is the joining of two suitably protected deoxynucleotides to form a dideoxynucleotide containing a phosphodiester bond. The diester method is well established and has been used to synthesize DNA molecules (Khorana, 1979).

[0119] Triester method. The main difference between the diester and triester methods is the presence in the latter of an extra protecting group on the phosphate atoms of the reactants and products (Itakura et al., 1975). The phosphate protecting group is usually a chlorophenyl group, which renders the nucleotides and polynucleotide intermediates soluble in organic solvents. Therefore purification's are done in chloroform solutions. Other improvements in the method include (i) the block coupling of trimers and larger oligomers, (ii) the extensive use of high-performance liquid chromatography for the purification of both intermediate and final products, and (iii) solid-phase synthesis.

[0120] Polynucleotide phosphorylase method. This is an enzymatic method of DNA synthesis that can be used to synthesize many useful oligodeoxynucleotides (Gillam et al., 1978; Gillam et al., 1979). Under controlled conditions, polynucleotide phosphorylase adds predominantly a single nucleotide to a short oligodeoxynucleotide. Chromatographic purification allows the desired single adduct to be obtained. At least a trimer is required to start the procedure, and this primer must be obtained by some other method. The polynucleotide phosphorylase method works and has the advantage that the procedures involved are familiar to most biochemists.

[0121] Solid-phase methods. Drawing on the technology developed for the solid-phase synthesis of polypeptides, it has been possible to attach the initial nucleotide to solid support material and proceed with the stepwise addition of nucleotides. All mixing and washing steps are simplified, and the procedure becomes amenable to automation. These syntheses are now routinely carried out using automatic DNA synthesizers.

[0122] Phosphoramidite chemistry (Beaucage, and Lyer, 1992) has become by far the most widely used coupling chemistry for the synthesis of oligonucleotides. As is well known to those skilled in the art, phosphoramidite synthesis of oligonucleotides involves activation of nucleoside phosphoramidite monomer precursors by reaction with an activating agent to form activated intermediates, followed by sequential addition of the activated intermediates to the growing oligonucleotide chain (generally anchored at one end to a suitable solid support) to form the oligonucleotide product.

[0123] 12. Expression Vectors

[0124] Other ways of creating nucleic acids of the invention include the use of a recombinant vector created through the application of recombinant nucleic acid technology known to those of skill in the art or as described herein. A recombinant vector may comprise a bridging or capture nucleic acid, particularly one that is a polynucleotide, as opposed to an oligonucleotide. An expression vector can be used create nucleic acids that are lengthy, for example, containing multiple targeting regions or relatively lengthy targeting regions, such as those greater than 100 residues in length.

[0125] The term “vector” is used to refer to a carrier nucleic acid molecule into which a nucleic acid sequence can be inserted for introduction into a cell where it can be replicated. A nucleic acid sequence can be “exogenous,” which means that it is foreign to the cell into which the vector is being introduced or that the sequence is homologous to a sequence in the cell but in a position within the host cell nucleic acid in which the sequence is ordinarily not found. Vectors include plasmids, cosmids, viruses (bacteriophage, animal viruses, and plant viruses), and artificial chromosomes (e.g., YACs). One of skill in the art would be well equipped to construct a vector through standard recombinant techniques (see, for example, Sambrook et al, 2001 and Ausubel et al., 1994, both incorporated herein by reference).

[0126] The term “expression vector” refers to any type of genetic construct comprising a nucleic acid coding for a RNA capable of being transcribed. Expression vectors can contain a variety of “control sequences,” which refer to nucleic acid sequences necessary for the transcription and possibly translation of an operable linked coding sequence in a particular host cell. In addition to control sequences that govern transcription (promoters and enhancers) and translation, vectors and expression vectors may contain nucleic acid sequences that serve other functions as well that are well known to those of skill in the art, such as screenable and selectable markers, ribosome binding site, multiple cloning sites, splicing sites, poly A sequences, origins of replication, and other sequences that allow expression in different hosts.

[0127] Numerous expression systems exist that comprise at least a part or all of the compositions discussed above. Prokaryote- and/or eukaryote-based systems can be employed for use with the present invention to produce nucleic acid sequences, or their cognate polypeptides, proteins and peptides. Many such systems are commercially and widely available.

[0128] The nucleotide and protein, polypeptide and peptide sequences for various genes have been previously disclosed, and may be found at computerized databases known to those of ordinary skill in the art. For example, the nucleotide sequences of rRNAs of various organisms are readily available. One such database is the National Center for Biotechnology Information's Genbank and GenPept databases (http://www.ncbi.nlm.nih.gov/). The coding regions for all or part of these known genes may be amplified and/or expressed using the techniques disclosed herein or by any technique that would be know to those of ordinary skill in the art.

[0129] 13. Nucleic Acid Arrays

[0130] Because the present invention provides efficient methods of enriching in mRNA, which can be used to make cDNA, the present invention extends to the use of cDNAs with arrays. The term “array” as used herein refers to a systematic arrangement of nucleic acid. For example, a cDNA population that is representative of a desired source (e.g., human adult brain) is divided up into the minimum number of pools in which a desired screening procedure can be utilized to detect a cDNA and which can be distributed into a single multi-well plate. Arrays may be of an aqueous suspension of a cDNA population obtainable from a desired mRNA source, comprising: a multi-well plate containing a plurality of individual wells, each individual well containing an aqueous suspension of a different content of a cDNA population. The cDNA population may include cDNA of a predetermined size. Furthermore, the cDNA population in all the wells of the plate may be representative of substantially all mRNAs of a predetermined size from a source. Examples of arrays, their uses, and implementation of them can be found in U.S. Pat. Nos. 6,329,209, 6,329,140, 6,324,479, 6,322,971, 6,316,193, 6,309,823, 5,412,087, 5,445,934, and 5,744,305, which are herein incorporated by reference.

[0131] The number of cDNA clones array on a plate may vary. For example, a population of cDNA from a desired source can have about 200,000-6,000,000 cDNAs, about 200,000-2,000,000, 300,000-700,000, about 400,000-600,000, or about 500,000 cDNAs, and combinations thereof. Such a population can be distributed into a small set of multi-well plates, such as a single 96-well plate or a single 384-well plate. For instance, when about 1000-10,000 cDNAs, preferably about 3,500-7,000, more preferably about 5,000, from a population are present in a single well of a 96-well or 384-well plate, PCR can be utilized to clone a single, target gene using a set of primers.

[0132] The term a “nucleic acid array” refers to a plurality of target elements, each target element comprising one or more nucleic acid molecules immobilized on one or more solid surfaces to which sample nucleic acids can be hybridized. The nucleic acids of a target element can contain sequence(s) from specific genes or clones, e.g. from the regions identified here. Other target elements will contain, for instance, reference sequences. Target elements of various dimensions can be used in the arrays of the invention. Generally, smaller, target elements are preferred. Typically, a target element will be less than about 1 cm in diameter. Generally element sizes are from 1 μm to about 3 mm, between about 5 μm and about 1 mm. The target elements of the arrays may be arranged on the solid surface at different densities. The target element densities will depend upon a number of factors, such as the nature of the label, the solid support, and the like. One of skill will recognize that each target element may comprise a mixture of nucleic acids of different lengths and sequences. Thus, for example, a target element may contain more than one copy of a cloned piece of DNA, and each copy may be broken into fragments of different lengths. The length and complexity of the nucleic acid fixed onto the target element is not critical to the invention. One of skill can adjust these factors to provide optimum hybridization and signal production for a given hybridization procedure, and to provide the required resolution among different genes or genomic locations. In various embodiments, target element sequences will have a complexity between about 1 kb and about 1 Mb, between about 10 kb to about 500 kb, between about 200 to about 500 kb, and from about 50 kb to about 150 kb.

[0133] Microarrays are known in the art and consist of a surface to which probes that correspond in sequence to gene products (e.g., cDNAs, mRNAs, cRNAs, polypeptides, and fragments thereof), can be specifically hybridized or bound at a known position. In one embodiment, the microarray is an array (i.e., a matrix) in which each position represents a discrete binding site for a product encoded by a gene (e.g., a protein or RNA), and in which binding sites are present for products of most or almost all of the genes in the organism's genome. In a preferred embodiment, the “binding site” (hereinafter, “site”) is a nucleic acid or nucleic acid analogue to which a particular cognate cDNA can specifically hybridize. The nucleic acid or analogue of the binding site can be, e.g., a synthetic oligomer, a full-length cDNA, a less-than full length cDNA, or a gene fragment.

[0134] A microarray may contains binding sites for products of all or almost all genes in the target organism's genome, but such comprehensiveness is not necessarily required. Usually the microarray will have binding sites corresponding to at least about 50% of the genes in the genome, often at least about 75%, more often at least about 85%, even more often more than about 90%, and most often at least about 99%. Preferably, the microarray has binding sites for genes relevant to the action of a drug of interest or in a biological pathway of interest. A “gene” is identified as an open reading frame (ORF) of preferably at least 50, 75, or 99 amino acids from which a messenger RNA is transcribed in the organism (e.g., if a single cell) or in some cell in a multicellular organism. The number of genes in a genome can be estimated from the number of mRNAs expressed by the organism, or by extrapolation from a well-characterized portion of the genome. When the genome of the organism of interest has been sequenced, the number of ORFs can be determined and mRNA coding regions identified by analysis of the DNA sequence.

[0135] The nucleic acid or analogue are attached to a solid support, which may be made from glass, plastic (e.g., polypropylene, nylon), polyacrylamide, nitrocellulose, or other materials. A preferred method for attaching the nucleic acids to a surface is by printing on glass plates, as is described generally by Schena et al., 1995a. See also DeRisi et al., 1996; Shalon et al., 1996; Schena et al., 1995b. Each of these articles is incorporated by reference in its entirety.

[0136] Other methods for making microarrays, e.g., by masking (Maskos et al., 1992), may also be used. In principal, any type of array, for example, dot blots on a nylon hybridization membrane (see Sambrook et al., 1989, which is incorporated in its entirety for all purposes), could be used, although, as will be recognized by those of skill in the art, very small arrays will be preferred because hybridization volumes will be smaller.

[0137] Labeled cDNA is prepared from mRNA by oligo dT-primed or random-primed reverse transcription, both of which are well known in the art (see e.g., Klug et al., 1987). Reverse transcription may be carried out in the presence of a dNTP conjugated to a detectable label, most preferably a fluorescently labeled dNTP. Alternatively, isolated mRNA can be converted to labeled antisense RNA synthesized by in vitro transcription of double-stranded cDNA in the presence of labeled dNTPs (Lockhart et al., 1996, which is incorporated by reference in its entirety for all purposes). In alternative embodiments, the cDNA or RNA probe can be synthesized in the absence of detectable label and may be labeled subsequently, e.g., by incorporating biotinylated dNTPs or rNTP, or some similar means (e.g., photo-cross-linking a psoralen derivative of biotin to RNAs), followed by addition of labeled streptavidin (e.g., phycoerythrin-conjugated streptavidin) or the equivalent.

[0138] Fluorescently-labeled probes can be used, including suitable fluorophores such as fluorescein, lissamine, phycoerythrin, rhodamine (Perkin Elmer Cetus), Cy2, Cy3, Cy3.5, Cy5, Cy5.5, Cy7, Fluor X (Amersham) and others (see, e.g., Kricka, 1992). It will be appreciated that pairs of fluorophores are chosen that have distinct emission spectra so that they can be easily distinguished. In another embodiment, a label other than a fluorescent label is used. For example, a radioactive label, or a pair of radioactive labels with distinct emission spectra, can be used (see Zhao et al., 1995; Pietu et al., 1996). However, because of scattering of radioactive particles, and the consequent requirement for widely spaced binding sites, use of radioisotopes is a less-preferred embodiment.

[0139] In one embodiment, labeled cDNA is synthesized by incubating a mixture containing 0.5 mM dGTP, dATP and dCTP plus 0.1 mM dTTP plus fluorescent deoxyribonucleotides (e.g., 0.1 mM Rhodamine 110 UTP (Perken Elmer Cetus) or 0.1 mM Cy3 dUTP (Amersham)) with reverse transcriptase (e.g., SuperScript™, Invitrogen Inc.) at 42° C. for 60 min.

[0140] III. Methods for Isolating and Depleting Targeted Nucleic Acids

[0141] Methods of the invention involve preparing a sample comprising a targeted nucleic acid, preparing a bridging nucleic acid, preparing a capture nucleic acid, incubating the sample with the bridging nucleic acid, incubating the sample with a capture nucleic acid, incubating the bridging nucleic acid with the capture nucleic acid, incubating compounds under conditions allowing for hybridization among complementary regions, washing the sample and/or the capture and/or bridging nucleic acids, and isolating the capture nucleic acids and any accompanying compounds (compounds that bind or hybridize directly or indirectly to the capture nucleic acids). Steps of the invention are not required to be in a particular order and thus, the invention covers methods in which the order of the steps varies.

[0142] Hybridization conditions are discussed earlier. Wash conditions may involve temperatures between 20° C. and 75° C., between 25° C. and 70° C., between 30° C. and 65° C., between 35° C. and 60° C., between 40° C. and 55° C., between 45° C. and 50° C., or at temperatures within the ranges specified.

[0143] Buffer conditions for hybridization of nucleic acid compositions are well known to those of skill in the art. It is specifically contemplated that isostabilizing agents may be employed in hybridization and wash buffers in methods of the invention. U.S. Ser. No. 09/854,412 describes the use of tetramethylammonium chloride (TMAC) and tetraethylammonium chloride (TEAC) in such buffers; this application is specifically incorporated by reference herein. The concentration of an isostabilizing agent in a hybridization (binding) buffer may be between about 1.0 M and about 5.0 M, is about 4.0 M, or is about 2.0 M. Also specifically contemplated is a wash solution with an isostabilizing agent concentration of between about 0.1 M and 3.0 M, including 0.1 M increments within the range. Wash buffers may or may not contain Tris. However, in some embodiments of the invention, the wash solution consists of water and no other salts or buffers. In some embodiments of the invention, the hybridizing or wash buffer may include guanidinium isothiocyanate, though in some embodiments this chemical is specifically contemplated to be absent. The concentration of guanidinium may be between about 0.4 M and about 3.0 M

[0144] A solution or buffer to elute targeted nucleic acids from the hybridizing nucleic acids (indirect or direct) may be implemented in some kits and methods of the invention. The elution buffer or solution can be an aqueous solution lacking salt, such as TE or water. Elution may occur at room temperature or it may occur at temperatures between 15° C. and 100° C., between 20° C. and 95° C., between 25° C. and 90° C., between 30° C. and 85° C., between 35° C. and 80° C., between 40° C. and 75° C., between 45° C. and 70° C., between 50° C. and 65° C., between 55° C. and 60° C., or at temperatures within the ranges specified.

[0145] A. Quantitation of RNA

[0146] 1. Assessing RNA Yield by UV Absorbance

[0147] The concentration and purity of RNA can be determined by diluting an aliquot of the preparation (usually a 1:50 to 1:100 dilution) in TE (10 mM Tris-HCl pH 8, 1 mM EDTA) or water, and reading the absorbance in a spectrophotometer at 260 nm and 280 nm.

[0148] An A₂₆₀ of 1 is equivalent to 40 μg RNA/ml. The concentration (μg/ml) of RNA is therefore calculated by multiplying the A₂₆₀ X dilution factor X 40 μg/ml. The following is a typical example:

[0149] The typical yield from 10 μg total RNA is 3-5 μg. If the sample is re-suspended in 25 μl, this means that the concentration will vary between 120 ng/μl and 200 ng/μl. One μl of the prep is diluted 1:50 into 49 μl of TE. The A₂₆₀=0.1. RNA concentration=0.1×50×40 μg/ml=200 μg/ml or 0.2 μg/μl. Since there are 24 μl of the prep remaining after using 1 μl to measure the concentration, the total amount of remaining RNA is 24 μl×0.2 μg/μl=4.8 μg.

[0150] 2. Assessing RNA Yield with RiboGreen®

[0151] Molecular Probes' RiboGreen® fluorescence-based assay for RNA quantitation can be employed to measure RNA concentration.

[0152] B. Denaturing Agarose Gel Electrophoresis

[0153] Many mRNAs form extensive secondary structure. Ribosomal RNA depletion may be evaluated by agarose gel electrophoresis. Because of this, it is best to use a denaturing gel system to analyze RNA samples. A positive control should be included on the gel so that any unusual results can be attributed to a problem with the gel or a problem with the RNA under analysis. RNA molecular weight markers, an RNA sample known to be intact, or both, can be used for this purpose. It is also a good idea to include a sample of the starting RNA that was used in the enrichment procedure.

[0154] Ambion's NorthernMax™ reagents for Northern Blotting include everything needed for denaturing agarose gel electrophoresis. These products are optimized for ease of use, safety, and low background, and they include detailed instructions for use. An alternative to using the NorthernMax reagents is to use a procedure described in “Current Protocols in Molecular Biology”, Section 4.9 (Ausubel et al., eds.), hereby incorporated by reference. It is more difficult and time-consuming than the Northern-Max method, but it gives similar results.

[0155] C. Agilent 2100 Bioanalyzer

[0156] 1. Evaluating rRNA Removal with the RNA 6000 LabChip

[0157] An effective method for evaluating rRNA removal utilizes RNA analysis with the Caliper RNA 6000 LabChip Kit and the Agilent 2100 Bioanalayzer. Follow the instructions provided with the RNA 6000 LabChip Kit for RNA analysis. This system performs best with RNA solutions at concentrations between 50 and 250 ng/μl. Loading 1 μl of a typical enriched RNA sample is usually adequate for good performance.

[0158] 2. Expected Results

[0159] In enriched mRNA samples from prokaryotes, the 16S and 23S rRNA peaks will be absent or present in only very small amounts. The peak calling feature of the software may fail to identify the peaks containing small quantities of leftover 16S and 23S rRNAs. A peak corresponding to 5S and tRNAs may be present depending on how the total RNA was initially purified. If RNA was purified by a glass fiber filter method prior to enrichment, this peak will be smaller. The size and shape of the 5S rRNA-tRNA peak is unchanged by some embodiments.

[0160] IV. Kits

[0161] Any of the compositions described herein may be comprised in a kit. In a non-limiting example, a bridging nucleic acid and a capture nucleic acid may be comprised in a kit. The kits will thus comprise, in suitable container means, a bridging nucleic acid and a capture nucleic of the present invention. It may also include one or more buffers, such as hybridization buffer or a wash buffer, compounds for preparing the sample, and components for isolating the capture nucleic acid via the nonreacting structure. Other kits of the invention may include components for making a nucleic acid array, and thus, may include, for example, a solid support.

[0162] The kits may comprise suitably aliquoted nucleic acid compositions of the present invention, whether labeled or unlabeled, as may be used to isolate, deplete, or separate a targeted nucleic acid. The components of the kits may be packaged either in aqueous media or in lyophilized form. The container means of the kits will generally include at least one vial, test tube, flask, bottle, syringe or other container means, into which a component may be placed, and preferably, suitably aliquoted. Where there are more than one component in the kit (bridging and capture nucleic acids may be packaged together), the kit also will generally contain a second, third or other additional container into which the additional components may be separately placed. However, various combinations of components may be comprised in a vial. The kits of the present invention also will typically include a means for containing the nucleic acids, and any other reagent containers in close confinement for commercial sale. Such containers may include injection or blow-molded plastic containers into which the desired vials are retained.

[0163] When the components of the kit are provided in one and/or more liquid solutions, the liquid solution is an aqueous solution, with a sterile aqueous solution being particularly preferred.

[0164] However, the components of the kit may be provided as dried powder(s). When reagents and/or components are provided as a dry powder, the powder can be reconstituted by the addition of a suitable solvent. It is envisioned that the solvent may also be provided in another container means.

[0165] The container means will generally include at least one vial, test tube, flask, bottle, syringe and/or other container means, into which the nucleic acid formulations are placed, preferably, suitably allocated. The kits may also comprise a second container means for containing a sterile, pharmaceutically acceptable buffer and/or other diluent.

[0166] The kits of the present invention will also typically include a means for containing the vials in close confinement for commercial sale, such as, e.g., injection and/or blow-molded plastic containers into which the desired vials are retained.

[0167] Such kits may also include components that facilitate isolation of the targeting molecule, such as filters, beads, or a magnetic stand. Such kits generally will comprise, in suitable means, distinct containers for each individual reagent or solution as well as for the targeting agent.

[0168] A kit will also include instructions for employing the kit components as well the use of any other reagent not included in the kit. Instructions may include variations that can be implemented.

[0169] Kits of the invention may also include one or more of the following, in addition to a capture nucleic acid and a bridging nucleic acid:

[0170] 1) Control RNA (E. coli or other appropriate RNA);

[0171] 2) Nuclease-free water;

[0172] 3) RNase-free containers, such as 1.5 ml tubes;

[0173] 4) RNase-free elution tubes;

[0174] 5) glycogen;

[0175] 6) ethanol;

[0176] 7) sodium acetate;

[0177] 8) ammonium acetate;

[0178] 9) magnetic stand or other magnetic field;

[0179] 10) agarose;

[0180] 11) nucleic acid size marker;

[0181] 12) RNase-free tube tips;

[0182] 13) and RNase or DNase inhibitors.

IV. EXAMPLES

[0183] The following examples are included to demonstrate preferred embodiments of the invention. It should be appreciated by those of skill in the art that the techniques disclosed in the examples which follow represent techniques discovered by the inventor to function well in the practice of the invention, and thus can be considered to constitute preferred modes for its practice. However, those of skill in the art should, in light of the present disclosure, appreciate that many changes can be made in the specific embodiments which are disclosed and still obtain a like or similar result without departing from the spirit and scope of the invention.

[0184] Furthermore, these examples are provided as one of many ways of implementing the claimed method and using the compositions of the invention. It is contemplated that the invention is not limited to the specific conditions set forth below, but that the conditions below provide examples of how to implement the invention.

Example 1 Materials

[0185] The following materials were used in the methods described herein for the selective removal of 16S and 23S rRNA and/or 18S and 28S rRNA, and hence mRNA enrichment, from total RNA. All steps are performed at room temperature unless otherwise indicated.

[0186] 1. Bridging Nucleic Acids

[0187] In the following examples, the bridging regions are the poly-A stretches in the respective oligonucleotides.

[0188] Targeting regions for prokaryotic 16S and 23S rRNAs were designed based on a sequence comparison of different rRNAs from different bacteria to E. coli rRNA with MegAlign sequence analysis software version 4.05 from DNA Star, Incorporated (FIG. 2). The targeting regions are shown, in the examples below, 3′ of the bridging regions. Thus, the targeting region encompasses the remaining, non-bridging region of each molecule described below. SEQ ID NOs are provided for the targeting regions of the bridging nucleic acids provided below (i.e., sequence of bridging regions not included in SEQ ID NO.). 16S prokaryotic rRNA bridging oligonucleotides d16S-358 (SEQ ID NO:1) 5′-AAAAAAAAAAAAAAAAAAACTGCTGCCTCCCGTAGGAGTCT-3′ d16S-537 (SEQ ID NO:2) 5′-AAAAAAAAAAAAAAAAAACGTATTACCGCGGCTGCTGGCAC-3′ d16S-548 (SEQ ID NO:3) 5′-AAAAAAAAAAAAAAAAAACGCCCAGTAATTCCGATTAACGC-3′ d16S-807 (SEQ ID NO:4) 5′-AAAAAAAAAAAAAAAAAATGGACTACCAGGGTATCTAATCC-3′ d16S-1092 (SEQ ID NO:5) 5′-AAAAAAAAAAAAAAAAAAGGGTTGCGCTCGTTGCGGGACTT-3′ d16S-3′  (SEQ ID NO:6) 5′-AAAAAAAAAAAAAAAAAATAAGGAGGTGATCCAACCGCAGG-3′ 23S prokaryotic rRNA bridging oligonucleotides d23S-488 (SEQ ID NO:7) 5′-AAAAAAAAAAAAAAAAAAGGTTCTTTTTCACTCCCCTCGCC-3′ d23S-581 (SEQ ID NO:8) 5′-AAAAAAAAAAAAAAAAAAGACCCATTATACAAAAGGTACGC-3′ d23S-1118 (SEQ ID NO:9) 5′-AAAAAAAAAAAAAAAAAAGCCCCGTTACATCTTCCGCGCAG-3′ d23S-1926 (SEQ ID NO:10) 5′-AAAAAAAAAAAAAAAAAACGACAAGGAATTTCGCTACCTTA-3′ d23S-1954 (SEQ ID NO:11) 5′-AAAAAAAAAAAAAAAAAAACTTACCCGACAAGGAATTTCGC-3′ d23S-2511 (SEQ ID NO:12) 5′-AAAAAAAAAAAAAAAAAAGAGCCGACATCGAGGTGCCAAAC-3′ d23S-3′  (SEQ ID NO:13) 5′-AAAAAAAAAAAAAAAAAAAAGGTTAAGCCTCACGGTTCATT-3′ d23S-1704 (SEQ ID NO:15) 5′-AAAAAAAAAAAAAAAAAACCCCTTCTCCCGAAGTTACGGGG-3′ d23S-1105 (SEQ ID NO:16) 5′-AAAAAAAAAAAAAAAAAAAGTGAGCTATTACGCTTTCTTT-3′ RNA oligo bridging oligonucleotide r23S-3′  (SEQ ID NO:14) 5′-AAAAAAAAAAAAAAAAAAAAAAGGUUAAGCGUCACGGUUCAUU-(inverted (dT))-3′ (inverted refers to bases attached 3′ to 3′) Eukaryotic 18S rRNA bridging oligonucleotides d18S-3711 (SEQ ID NO:17) AAA AAA AAA AAA AAA AAA TAC CGG CCG TGC GTA CTT AGA CA d18S-4238 (SEQ ID NO:18) AAA AAA AAA AAA AAA AAA TGC CCT CCA ATG GAT CCT CGT TA d18S-5482 (SEQ ID NO:19) AAA AAA AAA AAA AAA AAA CTA CGG AAA CCT TGT TAC GAC TT Eukaryotic 28S rRNA bridging oligonucleotides d28S-11599 (SEQ ID NO:20) AAA AAA AAA AAA AAA AAA GAG CAC TGG GCA GAA ATC ACA TC d28S-7979 (SEQ ID NO:21) AAA AAA AAA AAA AAA AAA GTT TCT TTT CCT CCG CTG ACT AA d28S-12533 (SEQ ID NO:22) AAA AAA AAA AAA AAA AAA TCC TCA GCC AAG CAC ATA CAC CA

[0189] 2. Binding Buffer (also Referred to as Hybridization Buffer)

[0190] 3 M TMAC, 10 mM Tris, (pH 7.0)

[0191] 3. Bridging Nucleic Acid Mixture

[0192] Mixtures of 16S, 23S, 18S, and/or 28S bridging oligonucleotides were used. All oligonucleotides were purchased from IDT and purified from polyacrylamide gels.

[0193] 4. Capture Nucleic Acid (Oligo(dT) MagBeads)

[0194] Seradyn MGOL #2815-2103.

[0195] 5. Wash Solution

[0196] 2 M TMAC, 6.67 mM Tris (pH 7.0) (this is a dilution of binding buffer).

Example 2 Methods for rRNA Depletion from Prokaryotic Total RNA

[0197] The following methods are provided by way of example for practicing methods of the invention. They have been performed and shown to effect methods of the invention. The invention is not intended to be limited to these protocols, and it is specifically contemplated that variations of the methods below may be employed that fall within the scope of the invention if they effect depletion, isolation, or separation of a targeted nucleic acid, particularly rRNA.

[0198] This example demonstrates the depletion of 16S and 23S rRNA from E. coli total RNA.

[0199] RNA/Bridging Nucleic Acid Mixture Annealing

[0200] RNA (10 μg/15 μl) was added to 200 μl of binding buffer. The bridging nucleic acid mixture consisted of d16S-807 (5 μM), d16S-1092 (5 μM), d23S-1954 (5 μM), d23S-2511 (5 μM). The bridging nucleic acid mixture (4 μl) was added to the RNA and the mixture was incubated at 70° C. for 10 minutes and then shifted to 37° C. for 30 minutes.

[0201] Thirty minutes was found to be an adequate time for the annealing step. Longer time periods can be used with no adverse effects. Between fifteen and 120 minutes have been used successfully in the methods of the invention.

[0202] Preparation of Capture Nucleic Acid

[0203] Capture nucleic acid (Oligo (dT) MagBeads, Seradyn) in storage buffer was mixed and 50 μl was removed to a separate tube. A magnetic stand was applied to the side of the tube to capture the magnetic beads and the supernatant was removed. The capture nucleic acid was equilibrated one time with distilled, deionized water (50 μl) and once with binding buffer (50 μl). The captured nucleic acid was captured again with a magnetic stand, and the binding buffer wash was removed. The magnetic beads were resuspended in 50 μl of binding buffer.

[0204] rRNA Capture

[0205] Following the 30 minute annealing of RNA with the bridging nucleic acid mixture, the capture nucleic acid was added and the mixture was incubated at room temperature for 15 minutes. A magnetic stand was then applied to the tube to capture the magnetic beads. The supernatant containing mRNA, 5S rRNA, and tRNAs was removed to another tube and saved. An optional washing step was performed next. The magnetic beads were washed with Wash Solution (100 μl) and captured again. The wash supernatant was removed and added to the original supernatant.

[0206] Fifteen minutes was found to be an adequate time for rRNA capture. Longer time periods can be used with no adverse effects. rRNA capture likley occurs rapidly, and capture times of 5 minutes—60 minutes have been used successfully in the methods of the invention.

[0207] Precipitating mRNA

[0208] mRNA, 5S rRNA, and tRNAs were precipitated by adding 1/10 volume of 3M NaOAc (pH 5.5) and 3 volumes of 100% EtOH and incubating at −20° C. for 60 minutes. The precipitated RNA was pelleted in a microfuge, washed with 70% EtOH, and resuspended in TE (pH 8.0).

[0209] Analysis of Purified mRNA

[0210] Purified mRNA was analyzed with the Caliper RNA 6000 LabChip kit on an Agilent Bioanalyzer. Purified RNA was compared with a control E. coli total RNA sample that was carried through the reaction as described above, except that the Bridging Nucleic Acid Mixture was left out. This assay system uses electrophoretic and electrokinetic separation in a capillary electrophoresis type system. The rRNAs appear as peaks on an electropherogram (FIG. 3). The percentage of a rRNA present in the sample is calculated form the area under the peak.

[0211] Under the protocol conditions described above, the 5S+tRNA peak area is essentially the same in the control and in experimental samples. The % of 16S or 23S rRNA removed was calculated using the ratios of 16S_(peak area)/5S_(peak) area and 23S_(peak area)/5S_(peak area). Enriched and control RNAs with similar 5S+tRNA peak areas were compared.

[0212] % 16S rRNA removed=(16S_(peak area)/5S_(peak area))_(no oligos)control−(16S_(peak area)/5S_(peak area)) _(experimental) X 100

[0213] (16S_(peak area/)5S_(peak)area)_(no oligos control)

[0214] A corresponding formula was used to calculate % 23S rRNA removed.

[0215] Electropherograms of RNA from a control reaction and from an experimental reaction after ribosomal RNA depletion are shown in FIG. 3 and FIG. 4.

Example 3 Evaluations of Efficacy with Prokaryotic Targets

[0216] The materials and methods of Examples 1 and 2 were employed to determine the efficiency of removal of 16S rRNA or 23S rRNA or both from E. coli total RNA. Changes in the parameters of the experiments are noted when appropriate. These experiments were performed to evaluate the efficacy of various bridging nucleic acids and reaction conditions.

[0217] The following results are from reactions that employed 10 μg of E. coli total RNA, 40 pmol of total 16S rRNA bridging nucleic acid, 40 pmol of total 23S rRNA bridging nucleic acid, and 50 μl of capture nucleic acid described in Example 1. % 16S Removed % 23S Removed Bridging Nucleic Acid average of 2 average of 2 16S/23S reactions reactions d16S-358/d23S-2511 96.48285 89.86496 d16S-537/d23S-1954 97.47974 91.32074 d16S-537/d23S-2511 97.48704 91.216  d16S-807/d23S-1954 95.79126 89.85388 d16S-807/d23S-2511 95.25362 91.06399 d16S-1092/d23S-1118 97.91265 96.50658 d16S-1092/d23S-1954 96.7473  89.40605 d16S-1092/d23S-2511 97.61689 91.5964  d16S-358/d23S-1954 96.74434 88.07242 d16S1092/d23S-1954 97.19134 98.44728 (20 pmol) d23S-2511 (20 pmol)

[0218] The following results are from reactions that employed 10 μg of E. coli total RNA, 26 pmol of 16S rRNA bridging nucleic acid, 26 pmol of 23S rRNA bridging nucleic acid, and 35 μl of capture nucleic acid described in Example 1. % 16S Removed Bridging Nucleic Acid average of 2 % 23S Removed 16S/23S reactions average of 2 reactions d16S-1092/d23S-1118 97.38534 95.02083 d16S-1092/d23S-1957 97.8291  90.798 

[0219] The following results are from reactions that employed 10 μg of E. coli total RNA, 75 pmol of 16S rRNA bridging nucleic acid, 75 pmol of 23S rRNA bridging nucleic acid, and 100 μl of capture nucleic acid described in Example 1. % 16S Removed Bridging Nucleic Acid average of 2 % 23S Removed 16S . . . 23S reactions average of 2 reactions d16S-1092 . . . d23S-1118 99.14812 99.11895 d16S-1092 . . . d23S-1954 98.79938 98.45245 d16S-1092 . . . d23S-2511 99.00567 98.84033

[0220] The following results are from reactions that employed 10 μg of E. coli total RNA, 37.5 pmol of 16S rRNA bridging nucleic acid, 37.5 pmol of 23S rRNA bridging nucleic acid, and 50 μl of capture nucleic acid described in Example 1. Bridging % 16S Removed % 23S Removed Nucleic Acid average of 2 average of 2 16S/23S reactions reactions d16S-1092/d23S-1118 98.95563 98.28748 d16S-1092/d23S-1954 97.83593 94.84438

[0221] The following results are from reactions that employed 10 μg of E. coli total RNA, 75 pmol of 16S rRNA bridging nucleic acid or 75 pmol of 23S rRNA bridging nucleic acid with 75 μl of capture nucleic acid described in Example 1. Bridging Nucleic Acid 16S/23S % 16S Removed % 23S Removed n.a./d23S-581 — 98.98529 n.a./d23S-581 — 98.87251 n.a./d23S-1118 — 93.62175 n.a./d23S-1118 — 91.4927  n.a./d23S-1954 — 98.68262 n.a./d23S-1954 — 99.03237 n.a./d23S-2511 — 99.31982 n.a./d23S-2511 — 99.13291 d16S-358/n.a. 97.65586 — d16S-358/n.a. 97.51393 — d16S-537/n.a. 99.16427 — d16S-537/n.a. 98.92345 — d16S-807/n.a. 98.0661  — d16S-807/n.a. 98.14292 —

[0222] The following results are from reactions that employed 5 μg of E. coli total RNA, 25 pmol of each 16S rRNA or 23S rRNA bridging nucleic acid, and 25 μl of capture nucleic acid described in Example 1. The rRNA/bridging nucleic acid annealing reaction was for 60 minutes at 37° C. Bridging Nucleic Acid 16S/23S % 16S Removed % 23S Removed n.a./d23S-488 — ˜100 n.a./d23S-1118 — ˜100 d16S-3′/d23S-488 89.024 94.228 d16S-548/d23S-488 ˜100 93.718 d16S-1092/d23S-488 ˜100 92.652

[0223] The following results are from reactions that employed 5 μg of E. coli total RNA, 16S rRNA bridging nucleic acid as indicated, 23S rRNA bridging nucleic acid as indicated, and 25 μl of capture nucleic acid described in Example 1. The rRNA/bridging nucleic acid annealing reaction was for 120 minutes at 37° C. Bridging Nucleic Acid 16S/23S % 16S Removed % 23S Removed d16S-3′ (25 pmol)/n.a. 89.137 — d16S-548 (25 pmol)/n.a. ˜100 — d16S-1092 (25 pmol)/n.a. ˜100 — d16S-3′ (25 pmol) ˜100 — d16S-548 (25 pmol)/n.a. d16S-3′ (25 pmol) ˜100 — d16S-1092 (25 pmol)/n.a. d16S-548 (25 pmol) ˜100 — d16S-1092 (25 pmol)n.a. d16S-548 (25 pmol)/ ˜100 ˜100 d23S-3′ (25 pmol) d16S-1092 (25 pmol)/ ˜100 ˜100 d23S-3′ (25 pmol) d16S-3′ (25 pmol)/ 92 ˜100 d23S-3′ (25 pmol)

Example 4 The Effect of Washing the Capture Nucleic Acid

[0224] The purpose of this experiment was to determine if washing the capture nucleic acid and combining the wash with the purified mRNA had an effect on the presence of rRNA in the purified mRNA sample. Reactions employed 10 μg of E. coli total RNA, 75 pmol d16S-1092, 75 pmol of d23S-d1118, and 100 μl of capture nucleic acid described in Example 1. The rRNA/bridging nucleic acid annealing reaction proceeded for 60 min at 37° C. After the nucleic acid capture step, the capture nucleic acid (with bound rRNA) was resuspended and washed with 100 μl of the indicated solution at room temperature for 5 minutes. The capture nucleic acid was re-captured with a magnetic stand and the supernatant was removed and combined with mRNA in the supernatant from the first capture. mRNA in the combined supernatants were precipitated with ethanol and evaluated with RNA 6000 Lab Chip assay for the presence of rRNAs. The percent of rRNA removal for the entire process is indicated in the table below. Wash % 16S Removed % 23S Removed 0.4 M TMAC 66.061 66.175 1.0 M TMAC 95.810 96.708 1.5 M TMAC ˜100 ˜100 2.0 M TMAC ˜100 ˜100

[0225] These results demonstrate that lowering the molarity of the TMAC wash solution increases the stringency of the rRNA capture reaction when the temperature is held constant at room temperature. The results also demonstrate that washing the capture nucleic acid magnetic beads with 1.5 and 2.0 M TMAC does not remove rRNA from the capture nucleic acid.

Example 5 Evaluation of Efficacy with Prokaryotic and Eukaryotic rRNA Targets

[0226] The purpose of this example was to evaluate efficacy of the methods of the invention for depleting 16S rRNA, 18S rRNA, 23S rRNA, and 28S rRNA from mixtures of prokaryotic and eukaryotic total RNA. Depletion methods were verified using various mammalian samples, including rat livers.

[0227] Equal amounts (2.5 μg) of E. coli total RNA and rat liver total RNA were mixed prior to the mRNA enrichment procedure. The bridging oligonucleotides employed were: d16S-1092 (10 pmol) d16S-807 (10 pmol) d23S-1954 (10 pmol) d23S-2511 (10 pmol) d18S-3711 (20 pmol) d28S-11599 (20 pmol)

[0228] The reaction used 50 μl of capture nucleic acid as described in Example 1. No wash step was employed. Otherwise the reaction was performed according to methods in Example 2. The results are shown in FIGS. 5A and 5B. Note that all rRNAs were depleted except the 5S and 5.8S rRNAs for which no bridging oligonucleotides were added.

Example 6 Evaluation of Efficacy with Human rRNA Targets

[0229] Additional experiments were done using human samples to evaluate the extent of human rRNA depletion using the bridging oligonucleotides shown below. Depletion of 18S rRNA and 28S rRNA was observed from human liver total RNA. rRNAs were depleted from human liver total RNA (5 μg). The bridging oligonucleotides employed were: d18S-3711 (40 pmol) d28S-11599 (40 pmol)

[0230] The reaction used 50 μl of capture nucleic acid as described in Example 1. No wash step was employed. Otherwise the reaction was performed according to Example 2.

[0231] The results are shown in FIGS. 6A and 6B. Note that all rRNAs (18S, 28S) were depleted except the 5S and 5.8S rRNAs for which no bridging oligonucleotides were added.

Example 7 Evaluation of Efficacy with Rat rRNA Targets

[0232] Additional experiments were done using rat samples to evaluate the extent of rat rRNA depletion using the bridging oligonucleotides shown below. Depletion of 18S rRNA and 28S rRNA was observed from rat liver total RNA. rRNAs were depleted from rat liver total RNA (5 μg). The bridging oligonucleotides employed were:

[0233] d18S-3711R-polyA (40 pmol)

[0234] d28S-11599R-polyA (40 pmol)

[0235] The reaction used 50 μl of capture nucleic acid as described in Example 1. No wash step was employed. Otherwise the reaction was performed according to Example 2.

[0236] The results are shown in FIGS. 7A and 7B. Note that all rRNAs (18S, 28S) were depleted except the 5S and 5.8S rRNAs for which no bridging oligonucleotides were added.

Example 8 Evaluation of Efficacy with Mouse rRNA Targets

[0237] Additional experiments were done using mouse samples to evaluate the extent of rat rRNA depletion using the bridging oligonucleotides shown below. Depletion of 18S rRNA and 28S rRNA was observed from mouse liver total RNA (5 μg). The bridging oligonucleotides employed were: d18S-3711R-polyA (40 pmol) d28S-11599R-polyA (40 pmol)

[0238] The reaction used 50 μl of capture nucleic acid as described in Example 1. No wash step was employed. Otherwise the reaction was performed according to Example 2.

[0239] The results are shown in FIGS. 8A and 8B. Note that all rRNAs (18S, 28S) were depleted except the 5S and 5.8S rRNAs for which no bridging oligonucleotides were added.

Example 9 Use of Purified E. coli mRNA in Gene Array Expression Analysis

[0240] mRNA was purified from total E. coli RNA (10 μg) using the methods of the invention as described in Example 2. A control reaction was also performed in which the bridging nucleic acid mixture was omitted form the reaction. Control total RNA and purified mRNA (1.5 μg) were added to 70 pmol random hexamers in a final volume of 7.25 μl. The mixture was heated at 70° C. for 10 minutes, then transferred to ice for 3 minutes. The following components were added to each reaction: 5 μl cDNA 1^(st) strand synthesis buffer (Invitrogen) 2.5 μl 0.1 M DTT 1.25 μl 10 mM dATP 1.25 μl 10 mM dGTP 1.25 μl 10 mM dTTP 5 μl 10 mCi/ml ³³P-dCTP (Perkin Elmer-NEN) 1 μl Superscript II reverse transcriptase (Invitrogen) 200 U/μl

[0241] The reactions were incubated at 42° C. for 120 minutes. Unincorporated nucleotides were removed from the reactions with a Qiaquick PCR cleanup column (Qiagen). The labeled cDNAs (3×10⁷ cpm/blot) were used to probe replicate portions of Panorama™ E. coli gene arrays, using hybridization buffers supplied by the array manufacturer (Sigma-Genosys). The arrays were washed and exposed to film. This example demonstrates a dramatic increase in hybridization signal (sensitivity) on gene arrays when labeled cDNA is prepared from bacterial mRNA, purified according to the methods of the invention, rather than from total RNA.

Example 10 Instructions for Use with Kit

[0242] The following instructions have been followed with a kit of the invention described below for the successful depletion of 16S and 23S rRNA from a sample comprising prokaryotic RNA populations. Bridging oligonucleotides with targeting regions complementary to 18S and 28S rRNA may be employed according to the method below to effect a similar result (as in Examples 5-8). Materials Provided with a Kit Embodiment 30 μl Control RNA 1.2 ml Capture Nucleic Acid [as in Example 1] 7 ml Binding Buffer [as in Example 1] 95 μl Bridging Oligonucleotide Mix [as in Example 2] 2.4 ml Wash Solution [as in Example 1] 1.75 ml Nuclease-free Water 50 ea RNase-free 1.5 ml tubes 25 ea RNase-free 2 ml Elution tubes 200 μl Glycogen (5 mg/ml) 875 μl 3 M NaOAc

[0243] Experimental Parameters

[0244] A. RNA Source

[0245] This mRNA enrichment procedure is designed to work with purified total RNA from many different bacteria, including both gram-positive and gram-negative species. The procedure was optimized with total E. coli RNA and has been found to remove 90-99% of the rRNA from Bacillus subtilis, Staphylococcus aureus, Prochlorococcus sp., Neisseria meningitidis, and Pseudomonas aeruginosa, for example. It is contemplated that any eubacterial species may be targeted using the methods and compositions of the invention.

[0246] This procedure is designed so that small RNAs (including tRNA and 5S rRNA) remain in the enriched mRNA population. However, if the loss of very small RNA species (<200 base) will not be an issue, the initial isolation of total RNA should be performed with Ambion's RNAQUEOUS KIT. The RNAQUEOUS KIT will remove most small RNA species and provide the highest possible level of mRNA enrichment. If small RNAs are of interest to the user, it is best to avoid glass fiber filter-based purification.

[0247] B. Precipitate RNA to Remove Salt and Concentrate if Necessary

[0248] Total RNA prepared from a solid-phase extraction method such as RNAQUEOUS can be used immediately after elution because such samples are unlikely to have high levels of salt. On the other hand, RNA isolated by methods that include organic extractions, for example using the products RNAWIZ, TRIZOL or ToTALLY RNA, may have a substantial amount of residual salt. If RNA from these types of procedures has been precipitated only a single time, we recommend doing a second alcohol precipitation and 70% EtOH wash to remove residual salt before starting the enrichment procedure.

[0249] The recommended maximum amount of RNA per reaction is 10 μg and the recommended maximum volume for the RNA is 15 μl. If the RNA sample is too dilute, it will be necessary to precipitate and concentrate the RNA to at least 10 μg/15 μl. Precipitate the RNA with:

[0250] 0.1 volume 5 M Ammonium Acetate or 3 M sodium acetate

[0251] 1 μl Glycogen (The glycogen acts as a carrier to increase precipitation efficiency from dilute RNA solutions; it is unnecessary for solutions with 200 μg RNA/ml)

[0252] 2.5 volumes 100% ethanol

[0253] a. Leave the precipitation mixture at −20° C. overnight, or quick-freeze it in either ethanol and dry ice, or in a −70° C. freezer for 30 minutes.

[0254] b. Recover the RNA by centrifugation at 12,000×g for 30 minutes at 4° C.

[0255] c. Carefully remove and discard the supernatant. The RNA pellet may not adhere tightly to the walls of the tubes, so we suggest removing the supernatant by gentle aspiration with a fine-tipped pipette.

[0256] d. Centrifuge the tube briefly a second time, and aspirate any additional fluid that collects with a fine-tipped pipette.

[0257] e. Add 1 ml 70% ethanol, and vortex the tube a few times. Repellet the RNA by microcentrifuging, for 10 minutes at 4° C. Remove supernatant carefully as in steps c and d above.

[0258] RNA should be dissolved in TE or Ambion's THE RNA STORAGE SOLUTION. It is important to accurately quantitate RNA so as not to overload the system. Ambion recommends using the RiboGreen RNA Quantitation Assay and Kit (Molecular Probes) or a high quality, calibrated spectrophotometer.

[0259] C. Save an Aliquot of Your Total RNA

[0260] If possible, retain a small aliquot (˜1-2 μg) of the total RNA used for comparison with enriched mRNA by gel electrophoresis after the procedure is finished.

[0261] Instructions

[0262] A. Anneal RNA and Bridging Oligonucleotide Mix

[0263] 1. Add RNA to Binding Buffer

[0264] Add total RNA (up to 10 μg total RNA in a maximum volume of 15 μl) to 200 μl Binding Buffer in a 1.5 ml tube provided with the kit. Close the tube and tap or vortex gently to mix.

[0265] 2. Add Bridging Oligonucleotide Mix to RNA

[0266] Add 4.0 μl of the Bridging Oligonucleotide Mix to the RNA in Binding Buffer. Close the tube and tap or vortex gently to mix. Pulse in a microcentrifuge very briefly to get mixture to bottom of tube.

[0267] 3. Incubate Reactions at 70° C. for 10 Minutes.

[0268] Incubating the mixture at 70° C. for 10 minutes denatures secondary structures in RNA, including the 16S and 23S rRNAs, allowing for maximal hybridization of the bridging oligonucleotides to the rRNAs.

[0269] 4. Incubate Reactions at 37° C. for 1 Hour.

[0270] Incubating the mixture at 37° C. for 1 hour allows for binding of the bridging oligonucleotides to the 16S and 23S rRNA. The Binding Buffer has been optimized to function specifically and efficiently at this temperature.

[0271] B. Prepare the Capture Nucleic Acid

[0272] During the 1 hour RNA/^(Bridging) Oligonucleotide Mix annealing step, prepare the Capture Nucleic Acid. The Capture Nucleic Acid is in a 1% (10 mg/ml) suspension, vortex the tube briefly before pipetting to be sure they are well suspended.

[0273] 1. Aliquot the Capture Nucleic Acid

[0274] For each 10 μg reaction remove 50 μl Capture Oligos to a 1.5 ml tube. Capture Nucleic Acid for up to 10 reactions can be processed in a single 1.5 ml tube.

[0275] 2. Wash the Capture Nucleic Acid Once with Water and Once with Binding Buffer

[0276] a. Capture the beads (Capture Nucleic Acid) by placing the tube on the Magnetic Stand. Leave the tube on the stand until all of the Capture Nucleic Acid is arranged inside the tube near the magnet. This will take ˜3 minutes for microfuge tubes.

[0277] b. Carefully remove the supernatant by aspiration, leaving the beads in the tube, and discard the supernatant.

[0278] c. Add Nuclease Free Water to the captured beads at a ratio of 50 μl/50 μl beads).

[0279] d. Remove the tube from the Magnetic Stand, resuspend the beads by gently vortexing briefly, recapture the beads with a Magnetic Stand, carefully aspirate the supernatant, leaving the beads in the tube, and discard the supernatant.

[0280] e. Add Binding Buffer to the captured beads at a ratio of 50 μl/50 μl beads).

[0281] f. Repeat step d.

[0282] 3. Resuspend the Capture Nucleic Acid in Binding Buffer

[0283] a. Add Binding Buffer to the captured beads at a ratio of 50 μl/50 μl beads).

[0284] b. Remove the tube from the Magnetic Stand, resuspend the beads by gently tapping the tube or very gentle vortexing.

[0285] c. Pulse spin in a microcentrifuge to get liquid to the bottom of the tube.

[0286] C. Capture the rRNA with Capture Nucleic Acid and Recover the Enriched mRNA

[0287] 1. Add Capture Nucleic Acid (50 μl/rxn) to RNA/Bridging Oligonucleotide Mix and Incubate at RT for 15 Minutes.

[0288] a After the 1 hour incubation at 37° C. (Step A.4) remove tubes to room temperature (RT) and immediately add 50 μl of the washed and equilibrated beads (Capture Nucleic Acid, from Step B.3c) to each purification reaction. Very gently vortex or tap tube to mix briefly and pulse spin in a microcentrifuge to get liquid to the bottom of the tube.

[0289] b. Incubate 15 minutes at RT. During this step the oligonucleotide sequence on the Capture Nucleic Acid anneals to the bridging oligonucleotides. The bridging oligonucleotides remain hybridized to the 16S and 23S rRNAs. The hybridization “sandwich” of bridging oligonucleotide and capture oligonucleotide (via the capture region on the capture oligo and the bridging region on the bridging oligo) is formed at this step.

[0290] 2. Recover the Supernatant Containing the Enriched mRNA.

[0291] a. Capture the beads by placing the tube on the Magnetic Stand. Leave the tube on the stand until all of the beads are arranged inside the tube near the magnet. This will take ˜3 minutes for microfuge tubes. Allow the beads to be completely captured by the magnet for at least 3 minutes.

[0292] b. Remove the supernatant by aspiration, being careful not to dislodge the beads. Put the supernatant into a 2 ml nipple bottom tube on ice and save. Do not be overly concerned if there seems to be beads in the removed supernatant. The excess can be removed at the end of the procedure. The supernatant contains the enriched mRNA sample.

[0293] 3. Wash the Oligo MagBeads with Wash Solution and Recover the Wash.

[0294] a. Add Wash Solution to the captured beads at a ratio of 100 μl Wash Solution/50 μl beads.

[0295] b. Remove the tube from the Magnetic Stand, resuspend the beads by gently vortexing briefly.

[0296] c. Incubate at RT for 5 minutes.

[0297] d. Recapture the beads with the Magnetic Stand as in step C.2a. Allow the beads to be completely captured by the magnet for at least 3 minutes.

[0298] e. Remove the supernatant by aspiration, being careful not to dislodge the beads. Put this supernatant in the 2 ml nipple bottom tube on ice with that from step C.2b.

[0299] D. Precipitate and Resuspend the Enriched mRNA in the Supernatant.

[0300] 1. Perform an EtOH Precipitation on the Collected Supernatant.

[0301] a. Add {fraction (1/10)} Volume 3M NaOAc (35 μl) and 5 mg/ml glycogen to a final concentration of 100 μg/ml (7 μl) to the supernatant from step C.3.e. (the supernatant volume should be ˜350 μl).

[0302] b. Briefly vortex the sample to mix.

[0303] c. Add 3 Vol. ice cold 100% EtOH (1175 μl) and mix well by vortexing the sample.

[0304] d. Precipitate the sample at −20° C. for at least 1 hour.

[0305] e. Centrifuge the sample for 30 min.@13,000 rpm.

[0306] f. Carefully decant the supernatant.

[0307] g. Add 750 ml ice cold 70% EtOH, vortex briefly, and centrifuge for 5 min. ® 13,000 rpm. Decant the supernatant.

[0308] h. Repeat step D.1.g.

[0309] i. After decanting the supernatant spin briefly to collect. Remove the remaining supernatant with a pipettor, being careful not to dislodge the pellet. Air dry for 5 min.

[0310] 2. Resuspend the Enriched mRNA in an Appropriate Buffer.

[0311] a. After the pellet has air dried for no more than 5 min. add 2 μl TE pH 8.0 (RNA STORAGE SOLUTION, 1 mM EDTA or Nuclease-Free ddH₂O could be substituted).

[0312] b. Allow the RNA to resuspend for 15 min. at room temperature. Vortex the sample vigorously to resuspend. Collect the sample by brief centrifugation. NOTE: If the pellet refuses to go into solution the sample can be incubated for 5 min. @ 70° C. This should help resuspend the pellet. NOTE: Often there will be beads remaining in the sample after the precipitation (This will cause the RNA solution to appear brownish in color). This can be remedied by applying the sample to the Magnetic stand for ˜3 min. and removing the supernatant to a new tube.

[0313] All of the compositions and methods disclosed and claimed herein can be made and executed without undue experimentation in light of the present disclosure. While the compositions and methods of this invention have been described in terms of preferred embodiments, it will be apparent to those of skill in the art that variations may be applied to the compositions and/or methods and in the steps or in the sequence of steps of the method described herein without departing from the concept, spirit and scope of the invention. More specifically, it will be apparent that certain agents that are both chemically and physiologically related may be substituted for the agents described herein while the same or similar results would be achieved. All such similar substitutes and modifications apparent to those skilled in the art are deemed to be within the spirit, scope and concept of the invention as defined by the appended claims.

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1 73 1 22 DNA Artificial Sequence Description of Artificial Sequence Synthetic Primer 1 ctgctgcctc ccgtaggagt ct 22 2 23 DNA Artificial Sequence Description of Artificial Sequence Synthetic Primer 2 cgtattaccg cggctgctgg cac 23 3 23 DNA Artificial Sequence Description of Artificial Sequence Synthetic Primer 3 cgcccagtaa ttccgattaa cgc 23 4 23 DNA Artificial Sequence Description of Artificial Sequence Synthetic Primer 4 tggactacca gggtatctaa tcc 23 5 23 DNA Artificial Sequence Description of Artificial Sequence Synthetic Primer 5 gggttgcgct cgttgcggga ctt 23 6 23 DNA Artificial Sequence Description of Artificial Sequence Synthetic Primer 6 taaggaggtg atccaaccgc agg 23 7 23 DNA Artificial Sequence Description of Artificial Sequence Synthetic Primer 7 ggttcttttt cactcccctc gcc 23 8 23 DNA Artificial Sequence Description of Artificial Sequence Synthetic Primer 8 gacccattat acaaaaggta cgc 23 9 23 DNA Artificial Sequence Description of Artificial Sequence Synthetic Primer 9 gccccgttac atcttccgcg cag 23 10 23 DNA Artificial Sequence Description of Artificial Sequence Synthetic Primer 10 cgacaaggaa tttcgctacc tta 23 11 22 DNA Artificial Sequence Description of Artificial Sequence Synthetic Primer 11 cttacccgac aaggaatttc gc 22 12 23 DNA Artificial Sequence Description of Artificial Sequence Synthetic Primer 12 gagccgacat cgaggtgcca aac 23 13 21 DNA Artificial Sequence Description of Artificial Sequence Synthetic Primer 13 ggttaagcct cacggttcat t 21 14 14 DNA Artificial Sequence Description of Artificial Sequence Synthetic Primer 14 ggaagcgcac ggca 14 15 23 DNA Artificial Sequence Description of Artificial Sequence Synthetic Primer 15 ccccttctcc cgaagttacg ggg 23 16 21 DNA Artificial Sequence Description of Artificial Sequence Synthetic Primer 16 gtgagctatt acgctttctt t 21 17 23 DNA Artificial Sequence Description of Artificial Sequence Synthetic Primer 17 taccggccgt gcgtacttag aca 23 18 23 DNA Artificial Sequence Description of Artificial Sequence Synthetic Primer 18 tgccctccaa tggatcctcg tta 23 19 23 DNA Artificial Sequence Description of Artificial Sequence Synthetic Primer 19 ctacggaaac cttgttacga ctt 23 20 23 DNA Artificial Sequence Description of Artificial Sequence Synthetic Primer 20 gagcactggg cagaaatcac atc 23 21 23 DNA Artificial Sequence Description of Artificial Sequence Synthetic Primer 21 gtttcttttc ctccgctgac taa 23 22 23 DNA Artificial Sequence Description of Artificial Sequence Synthetic Primer 22 tcctcagcca agcacataca cca 23 23 1427 DNA Bacillus subtilis modified_base (554)..(873) N = A, C, G or T/U 23 gagagtttga tcctggctca ggacgaacgc tggcggcgtg cctaatacat gcaagtcgag 60 cggacagatg ggagcttgct ccctgatgtt agcggcggac gggtgagtaa cacgtgggta 120 acctgcctgt aagactggga taactccggg aaaccggggc taataccgga tggttgtttg 180 aaccgcatgg ttcaaacata aaaggtggct tcggctacca cttacagatg gacccgcggc 240 gcattagcta gttggtgagg taacggctca ccaaggcaac gatgcgtagc cgacctgaga 300 gggtgatcgg ccacactggg actgagacac ggcccagact cctacgggag gcagcagtag 360 ggaatcttcc gcaatggacg aaagtctgac ggagcaacgc cgcgtgagtg atgaaggttt 420 tcggatcgta aagctctgtt gttagggaag aacaagtacc gttcgaatag ggcggtacct 480 tgacggtacc taaccagaaa gccacggcta actacgtgcc agcagccgcg gtaatacgta 540 ggtggcaagc gttntccgga attattgggc gtaaagggct cgcaggcggt ttcttaagtc 600 tgatgtgaaa gcccccggct caaccgggga gggtcattgg aaactgggga acttgagtgc 660 agaagaggag agtggaattc cacgtgtngc ggtgaaatgc gtagagatgt ggaggaacac 720 cagtggcgaa ggcgactctc tggtctgtaa ctgacgctga ggagcgaaag cgtggggagc 780 gaacaggatt agataccctg gtagtccacg ccgtaaacga tgagtgctaa gtgttagggg 840 gtttccgccc cttagtgctg cagtaacgca ttnagcactc cgcctgggga gtacggtcgc 900 aagactgaaa ctcaaaggaa ttgacggggg ccgcacaagc ggtggagcat gtggtttaat 960 tcgaagcaac gcgaagaacc ttaccaggtc ttgacatcct ctgacaatcc tagagatagg 1020 acgtcttcgg gggcagagtg acaggtggtg catggttgtc gtcagctcgt gtcgtgagat 1080 gttgggttaa gtcccgcaac gagcgcaacc ctggatctta gttgccagca ttcagttggg 1140 cactctaagg tgactgccgg tgacaaaccg gaggaaggtg gggatgacgt caaatcatca 1200 tgccccttat gacctgggct acacacgtgc tacaatggac agaacaaagg gcagcgaaac 1260 cgcgaggtta agccaatccc acaaatctgt tctcagttcg gatcgcagtc tgcaactcga 1320 ctgcgtgaag ctggaatcgc tagtaatcgc ggatcagcat gccgcggtga atacgttccc 1380 gggccttgta cacaccgccc gtcacaccac gagagtttgt aacaccc 1427 24 1544 DNA Bacillus anthracis 24 gtttgatcct ggctcaggat gaacgctggc ggcgtgccta atacatgcaa gtcgagcgaa 60 tggattaaga gcttgctctt atgaagttag cggcggacgg gtgagtaaca cgtgggtaac 120 ctgcccataa gactgggata actccgggaa accggggcta ataccggata acattttgaa 180 ccgcatggtt cgaaattgaa aggcggcttc ggctgtcact tatggatgga cccgcgtcgc 240 attagctagt tggtgaggta acggctcacc aaggcaacga tgcgtagccg acctgagagg 300 gtgatcggcc acactgggac tgagacacgg cccagactcc tacgggaggc agcagtaggg 360 aatcttccgc aatggacgaa agtctgacgg agcaacgccg cgtgagtgat gaaggctttc 420 gggtcgtaaa actctgttgt tagggaagaa caagtgctag ttgaataagc tggcaccttg 480 acggtaccta accagaaagc cacggctaac tacgtgccag cagccgcggt aatacgtagg 540 tggcaagcgt tatccggaat tattgggcgt aaagcgcgcg caggtggttt cttaagtctg 600 atgtgaaagc ccacggctca accgtggagg gtcattggaa actgggagac ttgagtgcag 660 aagaggaaag tggaattcca tgtgtagcgg tgaaatgcgt agagatatgg aggaacacca 720 gtggcgaagg cgactttctg gtctgtaact gacactgagg cgcgaaagcg tggggagcaa 780 acaggattag ataccctggt agtccacgcc gtaaacgatg agtgctaagt gttagagggt 840 ttccgccctt tagtgctgaa gttaacgcat taagcactcc gcctggggag tacggccgca 900 aggctgaaac tcaaaggaat tgacgggggc ccgcacaagc ggtggagcat gtggtttaat 960 tcgaagcaac gcgaagaacc ttaccaggtc ttgacatcct ctgacaaccc tagagatagg 1020 gcttctcctt cgggagcaga gtgacaggtg gtgcatggtt gtcgtcagct cgtgtcgtga 1080 gatgttgggt taagtcccgc aacgagcgca acccttgatc ttagttgcca tcattaagtt 1140 gggcactcta aggtgactgc cggtgacaaa ccggaggaag gtggggatga cgtcaaatca 1200 tcatgcccct tatgacctgg gctacacacg tgctacaatg gacggtacaa agagctgcaa 1260 gaccgcgagg tggagctaat ctcataaaac cgttctcagt tcggattgta ggctgcaact 1320 cgcctacatg aagctggaat cgctagtaat cgcggatcag catgccgcgg tgaatacgtt 1380 cccgggcctt gtacacaccg cccgtcacac cacgagagtt tgtaacaccc gaagtcggtg 1440 gggtaacctt tttggagcca gccgcctaag gtgggacaga tgattggggt gaagtcgtaa 1500 caaggtagcc gtatcggaag gtgcggctgg atcacctcct ttct 1544 25 1449 DNA Enterococcus faecalis 25 cgaacgctgg cggcgtgcct aatacatgca agtcgaacgc ttctttcctc ccgagtgctt 60 gcactcaatt ggaaagagga gtggcggacg ggtgagtaac acgtgggtaa cctacccatc 120 agagggggat aacacttgga aacaggtgct aataccgcat aacagtttat gccgcatggc 180 ataagagtga aaggcgcttt cgggtgtcgc tgatggatgg acccgcggtg cattagctag 240 ttggtgaggt aacggctcac caaggccacg atgcatagcc gacctgagag ggtgatcggc 300 cacactggga ctgagacacg gcccagactc ctacgggagg cagcagtagg gaatcttcgg 360 caatggacga aagtctgacc gagcaacgcc gcgtgagtga agaaggtttt cggatcgtaa 420 aactctgttg ttagagaaga acaaggacgt tagtaactga acgtcccctg acggtatcta 480 accagaaagc cacggctaac tacgtgccag cagccgcggt aatacgtagg tggcaagcgt 540 tgtccggatt tattgggcgt aaagcgagcg caggcggttt cttaagtctg atgtgaaagc 600 ccccggctca accggggagg gtcattggaa actgggagac ttgagtgcag aagaggagag 660 tggaattcca tgtgtagcgg tgaaatgcgt agatatatgg aggaacacca gtggcgaagg 720 cggctctctg gtctgtaact gacgctgagg ctcgaaagcg tggggagcaa acaggattag 780 ataccctggt agtccacgcc gtaaacgatg agtgctaagt gttggagggt ttccgccctt 840 cagtgctgca gcaaacgcat taagcactcc gcctggggag tacgaccgca aggttgaaac 900 tcaaaggaat tgacgggggc ccgcacaagc ggtggagcat gtggtttaat tcgaagcaac 960 gcgaagaacc ttaccaggtc ttgacatcct ttgaccactc tagagataga gctttccctt 1020 cggggacaaa gtgacaggtg gtgcatggtt gtcgtcagct cgtgtcgtga gatgttgggt 1080 taagtcccgc aacgagcgca acccttattg ttagttgcca tcatttagtt gggcactcta 1140 gcgagactgc cggtgacaaa ccggaggaag gtggggatga cgtcaaatca tcatgcccct 1200 tatgacctgg gctacacacg tgctacaatg ggaagtacaa cgagtcgcta gaccgcgagg 1260 tcatgcaaat ctcttaaagc ttctctcagt tcggattgca ggctgcaact cgcctgcatg 1320 aagccggaat cgctagtaat cgcggatcag cacgccgcgg tgaatacgtt cccgggcctt 1380 gtacacaccg cccgtcacac cacgagagtt tgtaacaccc gaagtcggtg aggtaacctt 1440 tttggagcc 1449 26 1548 DNA Lactococcus lactis 26 tttatttgag agtttgatcc tggctcagga cgaacgctgg cggcgtgcct aatacatgca 60 agttgagcgc tgaaggttgg tacttgtacc gactggatga gcagcgaacg ggtgagtaac 120 gcgtggggaa tctgcctttg agcgggggac aacatttgga aacgaatgct aataccgcat 180 aaaaacttta aacacaagtt ttaagtttga aagatgcaat tgcatcactc aaagatgatc 240 ccgcgttgta ttagctagtt ggtgaggtaa aggctcacca aggcgatgat acatagccga 300 cctgagaggg tgatcggcca cattgggact gagacacggc ccaaactcct acgggaggca 360 gcagtaggga atcttcggca atggacgaaa gtctgaccga gcaacgccgc gtgagtgaag 420 aaggttttcg gatcgtaaaa ctctgttggt agagaagaac gttggtgaga gtggaaagct 480 catcaagtga cggtaactac ccagaaaggg acggctaact acgtgccagc agccgcggta 540 atacgtaggt cccgagcgtt gtccggattt attgggcgta aagcgagcgc aggtggttta 600 ttaagtctgg tgtaaaaggc agtggctcaa ccattgtatg cattggaaac tggtagactt 660 gagtgcagga gaggagagtg gaattccatg tgtagcggtg aaatgcgtag atatatggag 720 gaacaccggt ggcgaaagcg gctctctggc ctgtaactga cactgaggct cgaaagcgtg 780 gggagcaaac aggattagat accctggtag tccacgccgt aaacgatgag tgctagatgt 840 agggagctat aagttctctg tatcgcagct aacgcaataa gcactccgcc tggggagtac 900 gaccgcaagg ttgaaactca aaggaattga cgggggcccg cacaagcggt ggagcatgtg 960 gtttaattcg aagcaacgcg aagaacctta ccaggtcttg acatactcgt gctattccta 1020 gagataggaa gttccttcgg gacacgggat acaggtggtg catggttgtc gtcagctcgt 1080 gtcgtgagat gttgggttaa gtcccgcaac gagcgcaacc cctattgtta gttgccatca 1140 ttaagttggg cactctaacg agactgccgg tgataaaccg gaggaaggtg gggatgacgt 1200 caaatcatca tgccccttat gacctgggct acacacgtgc tacaatggat ggtacaacga 1260 gtcgcgagac agtgatgttt agctaatctc ttaaaaccat tctcagttcg gattgtaggc 1320 tgcaactcgc ctacatgaag tcggaatcgc tagtaatcgc ggatcagcac gccgcggtga 1380 atacgttccc gggccttgta cacaccgccc gtcacaccac gggagttggg agtacccgaa 1440 gtaggttgcc taaccgcaag gagggcgctt cctaaggtaa gaccgatgac tggggtgaag 1500 tcgtaacaag gtagccgtat cggaaggtgc ggctggatca cctccttt 1548 27 1524 DNA Listeria monocytogenes 27 gcctgcaggt cgacaacaga gtttgatcat ggctcaggac gaacgctggc ggcgtgccta 60 atacatgcaa gtcgaacgaa cggaggaaga gcttgctctt ccaaagttag tggcggacgg 120 gtgagtaaca cgtgggcaac ctgcctgtaa gttggggata actccgggaa accggggcta 180 ataccgaatg ataaagtgtg gcgcatgcca cgcttttgaa agatggtttc ggctatcgct 240 tacagatggg cccgcggtgc attagctagt tggtagggta atggcctacc aaggcaacga 300 tgcatagccg acctgagagg gtgatcggcc acactgggac tgagacacgg cccagactcc 360 tacgggaggc agcagtaggg aatcttccgc aatggacgaa agtctgacgg agcaacgccg 420 cgtgtatgaa gaaggttttc ggatcgtaaa gtactgttgt tagagaagaa caaggataag 480 agtaactgct tgtcccttga cggtatctaa ccagaaagcc acggctaact acgtgccagc 540 agccgcggta atacgtaggt ggcaagcgtt gtccggattt attgggcgta aagcgcgcgc 600 aggcggtctt ttaagtctga tgtgaaagcc cccggcttaa ccggggaggg tcattggaaa 660 ctggaagact ggagtgcaga agaggagagt ggaattccac gtgtagcggt gaaatgcgta 720 gatatgtgga ggaacaccag tggcgaaggc gactctctgg tctgtaactg acgctgaggc 780 gcgaaagcgt ggggagcaaa caggattaga taccctggta gtccacgccg taaacgatga 840 gtgctaagtg ttagggggtt tccgcccctt agtgctgcag ctaacgcatt aagcactctg 900 cctggggagt acgaccgcaa ggttgaaact caaaggaatt gacgggggcc cgcacaagcg 960 tggagcatgt ggtttaattc gaagcaacgc gaagaacctt accaggtctt gacatccttt 1020 gaccactctg gagacagagc tttcccttcg ggacaaagtg acaggtggtg catggttgtc 1080 gtcagctcgt gtcgtgagat gttgggttaa gtcccgcaac gagcgcaacc cttgatttta 1140 gttgccagca tttagttggg cactctaaag tgactgccgg tgcaagccga ggaaggtggg 1200 gatgacgtca aatcatcatg ccccttatga cctgggctac acacgtgcta caatggatag 1260 tacaaagggt cgcgaagccg cgaggtggag ctaatcccat aaaactattc tcagttcgga 1320 ttgtaggctg caactcgcct acatgaagcc ggaatcgcta gtaatcgtgg atcagcatgc 1380 cacggtgagt acgttcccgg gccttgtaca caccgcccgt cacaccacga gagtttgtaa 1440 cacccgaagt cggtagggta acctttatgg agccagccgc cgaaggtggg acagataatt 1500 ggggtgaagt cgtaacaagg taaa 1524 28 1555 DNA Staphylococcus aureus 28 ttttatggag agtttgatcc tggctcagga tgaacgctgg cggcgtgcct aatacatgca 60 agtcgagcga acggacgaga agcttgcttc tctgatgtta gcggcggacg ggtgagtaac 120 acgtggataa cctacctata agactgggat aacttcggga aaccggagct aataccggat 180 aatattttga accgcatggt tcaaaagtga aagacggtct tgctgtcact tatagatgga 240 tccgcgctgc attagctagt tggtaaggta acggcttacc aaggcaacga tacgtagccg 300 acctgagagg gtgatcggcc acactggaac tgagacacgg tccagactcc tacgggaggc 360 agcagtaggg aatcttccgc aatgggcgaa agcctgacgg agcaacgccg cgtgagtgat 420 gaaggtcttc ggatcgtaaa actctgttat tagggaagaa catatgtgta agtaactgtg 480 cacatcttga cggtacctaa tcagaaagcc acggctaact acgtgccagc agccgcggta 540 atacgtaggt ggcaagcgtt atccggaatt attgggcgta aagcgcgcgt aggcggtttt 600 ttaagtctga tgtgaaagcc cacggctcaa ccgtggaggg tcattggaaa ctggaaaact 660 tgagtgcaga agaggaaagt ggaattccat gtgtagcggt gaaatgcgca gagatatgga 720 ggaacaccag tggcgaaggc gactttctgg tctgtaactg acgctgatgt gcgaaagcgt 780 ggggatcaaa caggattaga taccctggta gtccacgccg taaacgatga gtgctaagtg 840 ttagggggtt tccgcccctt agtgctgcag ctaacgcatt aagcactccg cctggggagt 900 acgaccgcaa ggttgaaact caaaggaatt gacggggacc cgcacaagcg gtggagcatg 960 tggtttaatt cgaagcaacg cgaagaacct taccaaatct tgacatcctt tgacaactct 1020 agagatagag ccttcccctt cgggggacaa agtgacaggt ggtgcatggt tgtcgtcagc 1080 tcgtgtcgtg agatgttggg ttaagtcccg caacgagcgc aacccttaag cttagttgcc 1140 atcattaagt tgggcactct aagttgactg ccggtgacaa accggaggaa ggtggggatg 1200 acgtcaaatc atcatgcccc ttatgatttg ggctacacac gtgctacaat ggacaataca 1260 aagggcagcg aaaccgcgag gtcaagcaaa tcccataaag ttgttctcag ttcggattgt 1320 agtctgcaac tcgactacat gaagctggaa tcgctagtaa tcgtagatca gcatgctacg 1380 gtgaatacgt tcccgggtat tgtacacacc gcccgtcaca ccacgagagt ttgtaacacc 1440 cgaagccggt ggagtaacct tttaggagct agccgtcgaa ggtgggacaa atgattgggg 1500 tgaagtcgta acaaggtagc cgtatcggaa ggtgcggctg gatcacctcc tttct 1555 29 1551 DNA Streptococcus mutans 29 agagtttgat cctggctcag gacgaacgct ggcggcgtgc ctaatacatg caagtgggac 60 gcaaggaaac acactgtgct tgcacaccgt gttttcttga gtcgcgaacg ggtgagtaac 120 gcgtaggtaa cctgcctatt agcgggggat aactattgga aacgatagct aataccgcat 180 aatattaatt attgcatgat aattgattga aagatgcaag cgcatcacta gtagatggac 240 ctgcgttgta ttagctagtt ggtaaggtaa gagcttacca aggcgacgat acatagccga 300 cctgagaggg tgatcggcca cactgggact gagacacggc ccagactcct acgggaggca 360 gcagtaggga atcttcggca atggacgaaa gtctgaccga gcaacgccgc gtgagtgaag 420 aaggttttcg gatcgtaaag ctctgttgta agtcaagaac gtgtgtgaga gtggaaagtt 480 cacacagtga cggtagctta ccagaaaggg acggctaact acgtgccagc agccgcggta 540 atacgtaggt cccgagcgtt gtccggattt attgggcgta aagggagcgc aggcggtcag 600 gaaagtctgg agtaaaaggc tatggctcaa ccatagtgtg ctctggaaac tgtctgactt 660 gagtgcagaa ggggagagtg gaattccatg tgtagcggtg aaatgcgtag atatatggag 720 gaacaccagt ggcgaaagcg gctctctggt ctgtcactga cgctgaggct cgaaagcgtg 780 ggtagcgaac aggattagat accctggtag tccacgccgt aaacgatgag tgctaggtgt 840 taggcccttt ccggggctta gtgccggagc taacgcaata agcactccgc ctggggagta 900 cgaccgcaag gttgaaactc aaaggaattg acgggggccc gcacaagcgg tggagcatgt 960 ggtttaattc gaagcaacgc gaagaacctt accaggtctt gacatcccga tgctattctt 1020 agagatagga agttacttcg gtacatcgga gacaggtggt gcatggttgt cgtcagctcg 1080 tgtcgtgaga tgttgggtta agtcccgcaa cgagcgcaac ccttattgtt agttgccatc 1140 attaagttgg gcactctagc gagactgccg gtaataaacc ggaggaaggt ggggatgacg 1200 tcaaatcatc atgcccctta tgacctgggc tacacacgtg ctacaatggt cggtacaacg 1260 agttgcgagc cggtgacggc aagctaatct ctgaaagccg atctcagttc ggattggagg 1320 ctgcaactcg cctccatgaa gtcggaatcg ctagtaatcg cggatcagca cgccgcggtg 1380 aatacgttcc cgggccttgt acacaccgcc cgtcacacca cgagagtttg taacacccga 1440 agtcggtgag gtaacctttt aagggccaag ccgcctaagg tgggatggat gattggggtg 1500 aagtcgtaac aaggtagccg tatcggaagg tgcggctgga tcacctcctt t 1551 30 1515 DNA Streptococcus pneumoniae 30 atttgatcct ggctcaggac gaacgctggc ggcgtgccta atacatgcaa gtagaacgct 60 gaaggaggag cttgcttctc tggatgagtt gcgaacgggt gagtaacgcg taggtaacct 120 gcctggtagc gggggataac tattggaaac gatagctaat accgcataag agtggatgtt 180 gcatgacatt tgcttaaaag gtgcacttgc atcactacca gatggacctg cgttgtatta 240 gctagttggt ggggtaacgg ctcaccaagg cgacgataca tagccgacct gagagggtga 300 tcggccacac tgggactgag acacgkccca gactcctacg ggaggcagca gtagggaatc 360 ttcggcaatg gacggaagtc tgaccgagca acgccgcgtg agtgaagaag gttttcggat 420 cgtaaagctc tgttgtaaga gaagaacgag tgtgagagtg gaaagttcac actgtgacgg 480 tatcttacca gaaagggacg gctaactacg tgccagcagc cgcggtaata cgtaggtccc 540 gagcgttgtc cggatttatt gggcgtaaag cgagcgcagg cggttagata agtctgaagt 600 taaaggctgt ggcttaacca tagtaggctt tggaaactgt ttaacttgag tgcaagaggg 660 gagagtggaa ttccatgtgt agcggtgaaa tgcgtagata tatggaggaa caccggtggc 720 gaaagcggct ctctggcttg taactgacgc tgaggctcga aagcgtgggg agcaaacagg 780 attagatacc ctggtagtcc acgctgtaaa cgatgagtgc taggtgttag accctttccg 840 gggtttagtg ccgtagctaa cgcattaagc actccgcctg gggagtacga ccgcaaggtt 900 gaaactcaaa ggaattgacg ggggcccgca caagcggtgg agcatgtggt ttaattcgaa 960 gcaacgcgaa gaaccttacc aggtcttgac atccctctga ccgctctaga gatagagttt 1020 tccttcggga cagaggtgac aggtggtgca tggttgtcgt cagctcgtgt cgtgagatgt 1080 tgggttaagt cccgcaacga gcgcaacccc tattgttagt tgccatcatt cagttgggca 1140 ctctagcgag actgccggta ataaaccgga ggaaggtggg gatgacgtca aatcatcatg 1200 ccccttatga cctgggctac acacgtgcta caatggctgg tacaacgagt cgcaagccgg 1260 tgacggcaag ctaatctctt aaagccagtc tcagttcgga ttgtaggctg caactcgcct 1320 acatgaagtc ggaatcgcta gtaatcgcgg atcagcacgc cgcggtgaat acgttcccgg 1380 gccttgtaca caccgcccgt cacaccacga gagtttgtaa cacccgaagt cggtgaggta 1440 accgtaagga gccagccgcc taaggtggga tagatgattg gggtgaagtc gtaacaaggt 1500 cagccgtttg ggaga 1515 31 1335 DNA Streptococcus pyogenes 31 gaacgggtga gtaacgcgta ggtaacctac ctcatagcgg gggataacta ttggaaacga 60 tagctaatac cgcataagag agactaacgc atgttagtaa tttaaaaggg gcaattgctc 120 cactatgaga tggacctgcg ttgtattagc tagttggtga ggtaaaggct caccaaggcg 180 acgatacata gccgacctga gagggtgatc ggccacactg ggactgagac acggcccaga 240 ctcctacggg aggcagcagt agggaatctt cggcaatggg ggcaaccctg accgagcaac 300 gccgcgtgag tgaagaaggt tttcggatcg taaagctctg ttgttagaga agaatgatgg 360 tgggagtgga aaatccacca agtgacggta actaaccaga aagggacggc taactacgtg 420 ccagcagccg cggtaatacg taggtcccga gcgttgtccg gatttattgg gcgtaaagcg 480 agcgcaggcg gttttttaag tctgaagtta aaggcattgg ctcaaccaat gtacgctttg 540 gaaactggag aacttgagtg cagaagggga gagtggaatt ccatgtgtag cggtgaaatg 600 cgtagatata tggaggaaca ccggtggcga aagcggctct ctggtctgta actgacgctg 660 aggctcgaaa gcgtggggag caaacaggat tagataccct ggtagtccac gccgtaaacg 720 atgagtgcta ggtgttaggc cctttccggg gcttagtgcc ggagctaacg cattaagcac 780 tccgcctggg gagtacgacc gcaaggttga aactcaaagg aattgacggg ggcccgcaca 840 agcggtggag catgtggttt aattcgaagc aacgcgaaga accttaccag gtcttgacat 900 cccgatgccc gctctagaga tagagtttta cttcggtaca tcggtgacag gtggtgcatg 960 gttgtcgtca gctcgtgtcg tgagatgttg ggttaagtcc cgcaacgagc gcaaccccta 1020 ttgttagttg ccatcattaa gttgggcact ctagcgagac tgccggtaat aaaccggagg 1080 aaggtgggga tgacgtcaaa tcatcatgcc ccttatgacc tgggctacac acgtgctaca 1140 atggttggta caacgagtcg caagccggtg acggcaagct aatctcttaa agccaatctc 1200 agttcggatt gtaggctgca actcgcctac atgaagtcgg aatcgctagt aatcgcggat 1260 cagcacgccg cggtgaatac gttcccgggc cttgtacaca ccgcccgtca caccacgaga 1320 gtttgtaaca cccga 1335 32 1465 DNA Mycobacterium avium modified_base (298)..(881) N = A, C, G or T/U 32 ggcggcgtgc ttaacacatg caagtcgaac ggaaaggcct cttcggaggt actcgagtgg 60 cgaacgggtg agtaacacgt gggcaatcta ccctgcactt cgggataagc ctgggaaact 120 gggtctaata ccggatagga cctcaagacg catgtcttct ggtggaaagc ttttgcggtg 180 tgggatgggc ccgcggccta tcagcttgtt ggtggggtga cggcctacca aggcgacgac 240 gggtagccgg cctgagaggg tgtccggcca cactgggact gagatacggc ccagactnct 300 acgggaggca gcagtgggga atattgcaca atgggcgcaa gcctgatgca gcgacgccgc 360 gtgggggatg acggccttcg ggttgtaaac ctctttcacc atcgacgaag gtccgggttt 420 tctcggattg acggtaggtg gagaagaagc accggccaac tacgtgccag cagccgcggt 480 aatacgtagg gtgcgagcgt tgtccggaat tactgggcgt aaagagctcg taggtggttt 540 gtcgcgttgt tcgtgaaatc tcacggctta actgtgagcg tgcgngcgat acgggcagac 600 tagagtactg caggggagac tggaattcct ggtgtagcgg tggaatgcgc agatatcagg 660 aggaacaccg gtggcgaagg cgggtctctg ggcagtaact gacgctgagg agcgaaagcg 720 tggggagcga acaggattag ataccctggt agtccacgnc gtaaacggtg ggtactaggt 780 gtgggtttcc ttccttggga tccgtgccgt agctaacgca ttaagtaccc cgcctgggga 840 gtacggncgc aaggctaaaa ctcaaaggaa ttgacggggg nccgcacaag cggcggagca 900 tgtggattaa ttcgatgcaa cgcgaagaac cttacctggg tttgacatgc acaggacgcg 960 tctagagata ggcgttccct tgtggcctgt gtgcaggtgg tgcatggctg tcgtcagctc 1020 gtgtcgtgag atgttgggtt aagtcccgca acgagcgcaa cccttgtctc atgttgccag 1080 cgggtaatgc cggggactcg tgagagactg ccggggtcaa ctcggaggaa ggtggggatg 1140 acgtcaagtc atcatgcccc ttatgtccag ggcttcacac atgctacaat ggccggtaca 1200 aagggctgcg atgccgtaag gttaagcgaa tccttttaaa gccggtctca gttcggattg 1260 gggtctgcaa ctcgacccca tgaagtcgga gtcgctagta atcgcagatc agcaacgctg 1320 cggtgaatac gttcccgggc cttgtacaca ccgcccgtca cgtcatgaaa gtcggtaaca 1380 cccgaagcca gtggcctaac ccttttggga gggagctgtc gaaggtggga tcggcgattg 1440 ggacgaagtc gtaacaaggt agccg 1465 33 1536 DNA Mycobacterium tuberculosis 33 tttgtttgga gagtttgatc ctggctcagg acgaacgctg gcggcgtgct taacacatgc 60 aagtcgaacg gaaaggtctc ttcggagata ctcgagtggc gaacgggtga gtaacacgtg 120 ggtgatctgc cctgcacttc gggataagcc tgggaaactg ggtctaatac cggataggac 180 cacgggatgc atgtcttgtg gtggaaagcg ctttagcggt gtgggatgag cccgcggcct 240 atcagcttgt tggtggggtg acggcctacc aaggcgacga cgggtagccg gcctgagagg 300 gtgtccggcc acactgggac tgagatacgg cccagactcc tacgggaggc agcagtgggg 360 aatattgcac aatgggcgca agcctgatgc agcgacgccg cgtgggggat gacggccttc 420 gggttgtaaa cctctttcac catcgacgaa ggtccgggtt ctctcggatt gacggtaggt 480 ggagaagaag caccggccaa ctacgtgcca gcagccgcgg taatacgtag ggtgcgagcg 540 ttgtccggaa ttactgggcg taaagagctc gtaggtggtt tgtcgcgttg ttcgtgaaat 600 ctcacggctt aactgtgagc gtgcgggcga tacgggcaga ctagagtact gcaggggaga 660 ctggaattcc tggtgtagcg gtggaatgcg cagatatcag gaggaacacc ggtggcgaag 720 gcgggtctct gggcagtaac tgacgctgag gagcgaaagc gtggggagcg aacaggatta 780 gataccctgg tagtccacgc cgtaaacggt gggtactagg tgtgggtttc cttccttggg 840 atccgtgccg tagctaacgc attaagtacc ccgcctgggg agtacggccg caaggctaaa 900 actcaaagga attgacgggg gcccgcacaa gcggcggagc atgtggatta attcgatgca 960 acgcgaagaa ccttacctgg gtttgacatg cacaggacgc gtctagagat aggcgttccc 1020 ttgtggcctg tgtgcaggtg gtgcatggct gtcgtcagct cgtgtcgtga gatgttgggt 1080 taagtcccgc aacgagcgca acccttgtct catgttgcca gcacgtaatg gtggggactc 1140 gtgagagact gccggggtca actcggagga aggtggggat gacgtcaagt catcatgccc 1200 cttatgtcca gggcttcaca catgctacaa tggccggtac aaagggctgc gatgccgcga 1260 ggttaagcga atccttaaaa gccggtctca gttcggatcg gggtctgcaa ctcgaccccg 1320 tgaagtcgga gtcgctagta atcgcagatc agcaacgctg cggtgaatac gttcccgggc 1380 cttgtacaca ccgcccgtca cgtcatgaaa gtcggtaaca cccgaagcca gtggcctaac 1440 cctcgggagg gagctgtcga aggtgggatc ggcgattggg acgaagtcgt aacaaggtag 1500 ccgtaccgga aggtgcggct ggatcacctc ctttct 1536 34 1536 DNA Escherichia coli 34 tttgtttgga gagtttgatc ctggctcagg acgaacgctg gcggcgtgct taacacatgc 60 aagtcgaacg gaaaggtctc ttcggagata ctcgagtggc gaacgggtga gtaacacgtg 120 ggtgatctgc cctgcacttc gggataagcc tgggaaactg ggtctaatac cggataggac 180 cacgggatgc atgtcttgtg gtggaaagcg ctttagcggt gtgggatgag cccgcggcct 240 atcagcttgt tggtggggtg acggcctacc aaggcgacga cgggtagccg gcctgagagg 300 gtgtccggcc acactgggac tgagatacgg cccagactcc tacgggaggc agcagtgggg 360 aatattgcac aatgggcgca agcctgatgc agcgacgccg cgtgggggat gacggccttc 420 gggttgtaaa cctctttcac catcgacgaa ggtccgggtt ctctcggatt gacggtaggt 480 ggagaagaag caccggccaa ctacgtgcca gcagccgcgg taatacgtag ggtgcgagcg 540 ttgtccggaa ttactgggcg taaagagctc gtaggtggtt tgtcgcgttg ttcgtgaaat 600 ctcacggctt aactgtgagc gtgcgggcga tacgggcaga ctagagtact gcaggggaga 660 ctggaattcc tggtgtagcg gtggaatgcg cagatatcag gaggaacacc ggtggcgaag 720 gcgggtctct gggcagtaac tgacgctgag gagcgaaagc gtggggagcg aacaggatta 780 gataccctgg tagtccacgc cgtaaacggt gggtactagg tgtgggtttc cttccttggg 840 atccgtgccg tagctaacgc attaagtacc ccgcctgggg agtacggccg caaggctaaa 900 actcaaagga attgacgggg gcccgcacaa gcggcggagc atgtggatta attcgatgca 960 acgcgaagaa ccttacctgg gtttgacatg cacaggacgc gtctagagat aggcgttccc 1020 ttgtggcctg tgtgcaggtg gtgcatggct gtcgtcagct cgtgtcgtga gatgttgggt 1080 taagtcccgc aacgagcgca acccttgtct catgttgcca gcacgtaatg gtggggactc 1140 gtgagagact gccggggtca actcggagga aggtggggat gacgtcaagt catcatgccc 1200 cttatgtcca gggcttcaca catgctacaa tggccggtac aaagggctgc gatgccgcga 1260 ggttaagcga atccttaaaa gccggtctca gttcggatcg gggtctgcaa ctcgaccccg 1320 tgaagtcgga gtcgctagta atcgcagatc agcaacgctg cggtgaatac gttcccgggc 1380 cttgtacaca ccgcccgtca cgtcatgaaa gtcggtaaca cccgaagcca gtggcctaac 1440 cctcgggagg gagctgtcga aggtgggatc ggcgattggg acgaagtcgt aacaaggtag 1500 ccgtaccgga aggtgcggct ggatcacctc ctttct 1536 35 1534 DNA Klebsiella pneumoniae modified_base (11)..(12) N = A, C, G or T/U 35 agagtttgat nntggctcag attgaacgct ggcggcaggc ctaacacatg caagtcgagc 60 ggtagcacag agagcttgct ctcgggtgac gagcggcgga cgggtgagta atgtctggga 120 aactgcctga tggaggggga taactactgg aaacggtagc taataccgca taacgtcgca 180 agaccaaagt gggggacctt cgggcctcat gccatcagat gtgcccagat gggattagct 240 agtaggtggg gtaacggctc acctaggcga cgatccctag ctggtctgag aggatgacca 300 gccacactgg aactgagaca cggtccagac tcctacggga ggcagcagtg gggaatattg 360 cacaatgggc gcaagcctga tgcagccatg ccgcgtgtgt gaagaaggcc ttcgggttgt 420 aaagcacttt cagcggggag gaaggcgatg aggttaataa cctcatcgat tgacgttacc 480 ctgcagaaga agcaccggct aactccgtgc cagcagccgc ggtaatacgg agggtgcaag 540 cgttaatcgg aattactggg cgtaaagcgc acgcaggcgg tctgtcaagt cggatgtgaa 600 atccccgggc tcaacctggg aactgcattc gaaactggca ggctagagtc ttgtagaggg 660 gggtagaatt ccaggtgtag cggtgaaatg cgtagagatc tggaggaata ccggtggcga 720 aggcggcccc ctggacaaag actgacgctc aggtgcgaaa gcgtggggag caaacaggat 780 tagataccct ggtagtccac gccgtaaacg atgtcgattt ggaggttgtg cccttgaggc 840 gtggcttccg gagctaacgc gttaaatcga ccgcctgggg agtacggccg caaggttaaa 900 actcaaatga attgacgggg gcccgcacaa gcggtggagc atgtggttta attcgatgca 960 acgcgaagaa ccttacctgg tcttgacatc cacagaactt tccagagatg gattggtgcc 1020 ttcgggaact gtgagacagg tgctgcatgg ctgtcgtcag ctcgtgttgt gaaatgttgg 1080 gttaagtccc gcaacgagcg caacccttat cctttgttgc cagcggttag gccgggaact 1140 caaaggagac tgccagtgat aaactggagg aaggtgggga tgacgtcaag tcatcatggc 1200 ccttacgacc agggctacac acgtgctaca atggcatata caaagagaag cgacctcgcg 1260 agagcaagcg gacctcataa agtatgtcgt agtccggatt ggagtctgca actcgactcc 1320 atgaagtcgg aatcgctagt aatcgtagat cagaatgcta cggtgaatac gttcccgggc 1380 cttgtacaca ccgcccgtca caccatggga gtgggttgca aaagaagtag gtagcttaac 1440 cttcgggagg gcgcttacca ctttgtgatt catgactggg gtgaagtcgt aacaaggtaa 1500 ccgtagggga acctgcggtt ggatcacctc cttt 1534 36 1485 DNA ACTINOBACCILUS ACTIN modified_base (208)..(1476) N = A, C, G or T/U 36 attgaagagt ttgatcatgg ctcagattga acgctggcgg caggcttaac acatgcaagt 60 cggacggtag caggagaaag cttgctttct tgctgacgag tggcggacgg gtgagtaatg 120 cttgggaatc tgtcttatgg agggggataa cgacgggaaa ctgtcgctaa taccgcgtag 180 agtcgggaga cgaaagtgcg ggactttntg gccgcatgcc atgagatgag cccaagtgtg 240 attaggtagt tggtggggta aaggcctacc aagccgacga tcgctagctg gtctgagagg 300 atggccagcc acaccgggac tgagacacgg cccngactcc tacgggaggc agcagtgggg 360 aatattgcgc aatgggggca accctgacgc agccatgccg cgtgaatgaa gaaggccttc 420 gggttgtaaa gttctttcgg tattgaggaa ggttggtgtg ttaatagcat gccaaattga 480 cgttaaatac agaagaagca ccggctaact ccgtgccagc agccgcggta atacgggggg 540 tgcgagcgtt aatcggaata actgggcgta aagggcacgt aggcggacct ttaagtgagg 600 tgtgaaatcc ccgggcttaa cctgggnatt gcatttcata ctgggggtct ggagtacttt 660 ngggagggnt agaattccac gtgtagcggt gaaatgcgta gagatgtgga ggaataccga 720 aggcgaaggc agccccttgg ggatgtactg acgctgatgt gcgaaagcgt ggggagcaaa 780 caggattaga taccctggta gtccacgctg taaacggtgt cgatttgggg attggggttt 840 agccctggtg cccgaagcta acgtgataaa tcgaccgcct ggggagtacg gccgcaaggt 900 taaaactcaa atgaattgac gggggcccgc acaagcggtg gagcatgtgg tttaattcga 960 tgcaacgcga agaaccttac ctactcttga catccgaaga agaactcaga gatgggtttg 1020 tgccttaggg agctttgaga caggtgctgc atggcngtcg tcagctcgtg ttgtgaaatg 1080 ttgggttaag tcccgcaacg agcgcaaccc ttatcctttg tggccagcga cgtggtcggg 1140 aactcaaagg agactgccgg tgataaaccg gaggaaggtg gggatgacgt caagtcatca 1200 tggcccttac gagtagggct acacacgtgc tacaatggcg tatacagagg gtaaccaacc 1260 agcgatgggg agtgaatctc agaaagtgcg tctaagttcg gattggagtc tgcaactcga 1320 ctccatgaag tcggaatcgc tagtaatcgc gaatcagaat gttgcggtga atacgttccc 1380 gggccttgta cacaccgccc gtcacaccat gggagtgggt tgtaccagaa gtggatagct 1440 gaaccgagag ggtggcgttt accacggtat gattcangac tgggg 1485 37 1487 DNA Haemophilus influenzae modified_base (1)..(1387) N = A, C, G or T/U 37 naattgaaga gtttgatcat ggctcagatt gaacgctggc ggcaggctta acacatgcaa 60 gtcgaacggt agcaggagaa agcttgcttt cttgctgacg agtggcggac gggtgagtaa 120 tgcttgggaa tctggcttat ggagggggat aacgacggga aactgtcgct aataccgcgt 180 attatcggaa gatgaaagtg cgggactgag aggccgcatg ccataggatg agcccaagtg 240 ggattaggta gttggtgggg taaatgccta ccaagcctgc gatctctagc tggtctgaga 300 ggatgaccag ccacactgga actgagacac ggtccagact cctacgggag gcagcagtgg 360 ggaatattgc gcnatggggg gaaccctgac gcagccatgc cgcgtgaatg aagaaggcct 420 tcgggttgta aagttctttc ggtattgagg aaggttgatg tgttaatagc acatcaaatt 480 gacgttaaat acagaagaag caccggctaa ctccgtgcca gcagccgcgg taatacggag 540 ngtgcgagcg ttaatcggaa taactgggcg taaagggcac gcaggcggtt atttaagtga 600 ggtgtgaaag ccccgggctt aacctgggna ttgcatttca gactgggtaa ctagagtact 660 ttagggaggg gtagaattcc acgtgtagcg gtgaaatgcg tagagatgtg gaggaatacc 720 gaaggcgaag gcagcccctt gggaatgtac tgacgctcat gtgcgaaagc gtggggagca 780 aacaggatta gataccctgg tagtccacgc tgtaaacgct gtcgatttgg gggttggggt 840 ttaactctgg cacccgtagc taacgtgata aatcgaccgc ctggggagta cggccgcaag 900 gttaaaactc aaatgaattg acgggggccn gcacaagcgg tggagcatgt ggtttaattc 960 gatgcaacgc gaagaacctt acctactctt gacatcctaa gaagagctca gagatgagct 1020 tgtgccttcg ggaacttaga gacaggtgct gcatggctgt cgtcagctcg tgttgtgaaa 1080 tgttgggtta agtcccgcaa cgagcgcaac ccttatcctt tgttgccagc gacttggtcg 1140 ggaactcaaa ggagactgcc agtgataaac tggaggaagg tngggatgac gtcaagtcat 1200 catggccctt acgagtaggg ctacacacgt gctacaatgg cgtatacaga gggaagcgaa 1260 gctgcgaggt ggagcgaatc tcataaagta cgtctaagtc cggattggag tctgcaactc 1320 gactccatga agtcggaatc gctagtaatc gcgaatcaga atgtcgcggt gaatacgttc 1380 ccgggcnttg tacacaccgc ccgtcacacc atgggagtgg gttgtaccag aagtagatag 1440 cttaaccttt tggagggcgt ttaccacggt atgattcatg actgggg 1487 38 1532 DNA Bordetella bronchiseptica 38 tgaactgaag agtttgatcc tggctcagat tgaacgctgg cgggatgctt tacacatgca 60 agtcggacgg cagcacgggc ttcggcctgg tggcgagtgg cgaacgggtg agtaatgtat 120 cggaacgtgc ccagtagcgg gggataacta cgcgaaagcg tggctaatac cgcatacgcc 180 ctacggggga aagcggggga ccttcgggcc tcgcactatt ggagcggccg atatcggatt 240 agctagttgg tggggtaacg gcctaccaag gcgacgatcc gtagctggtt tgagaggacg 300 accagccaca ctgggactga gacacggccc agactcctac gggaggcagc agtggggaat 360 tttggacaat gggggcaacc ctgatccagc catcccgcgt gtgcgatgaa ggccttcggg 420 ttgtaaagca cttttggcag gaaagaaacg gcacgggcta atatcctgtg caactgacgg 480 tacctgcaga ataagcaccg gctaactacg tgccagcagc cgcggtaata cgtagggtgc 540 aagcgttaat cggaattact gggcgtaaag cgtgcgcagg cggttcggaa agaaagatgt 600 gaaatcccag ggcttaacct tggaactgca tttttaacta ccgggctaga gtgtgtcaga 660 gggaggtgga attccgcgtg tagcagtgaa atgcgtagat atgcggagga acaccgatgg 720 cgaaggcagc ctcctgggat aacactgacg ctcatgcacg aaagcgtggg gagcaaacag 780 gattagatac cctggtagtc cacgccctaa acgatgtcaa ctagctgttg gggccttcgg 840 gccttggtag cgcagctaac gcgtgaagtt gaccgcctgg ggagtacggt cgcaagatta 900 aaactcaaag gaattgacgg ggacccgcac aagcggtgga tgatgtggat taattcgatg 960 caacgcgaaa aaccttacct acccttgaca tgtctggaat cccgaagaga tttgggagtg 1020 ctcgcaagag aaccggaaca caggtgctgc atggctgtcg tcagctcgtg tcgtgagatg 1080 ttgggttaag tcccgcaacg agcgcaaccc ttgtcattag ttgctacgaa agggcactct 1140 aatgagactg ccggtgacaa accggaggaa ggtggggatg acgtcaagtc ctcatggccc 1200 ttatgggtag ggcttcacac gtcatacaat ggtcgggaca gagggtcgcc aacccgcgag 1260 ggggagccaa tcccagaaac ccgatcgtag tccggatcgc agtctgcaac tcgactgcgt 1320 gaagtcggaa tcgctagtaa tcgcggatca gcatgtcgcg gtgaatacgt tcccgggtct 1380 tgtacacacc gcccgtcaca ccatgggagt gggttttacc agaagtagtt agcctaaccg 1440 caaggggggc gattaccacg gtaggattca tgactggggt gaagtcgtaa caaggtagcc 1500 gtatcggaag gtgcggctgg atcacctcct tt 1532 39 1485 DNA Bordetella parapertussis 39 attgaacgct ggcgggatgc tttacacatg caagtcggac ggcagcacgg gcttcggcct 60 ggtggcgagt ggcgaacggg tgagtaatgt atcggaacgt gcccagtagc gggggataac 120 tacgcgaaag cgtggctaat accgcatacg ccctacgggg gaaagcgggg gactttcggg 180 cctcgcacta ttggagcggc cgatatcgga ttagctagtt ggtggggtaa cggcctacca 240 aggcgacgat ccgtagctgg tttgagagga cgaccagcca cactgggact gagacacggc 300 ccagactcct acgggaggca gcagtgggga attttggaca atgggggcaa ccctgatcca 360 gccatcccgc gtgtgcgatg aaggccttcg ggttgtaaag cacttttggc aggaaagaaa 420 cggcacgggc taatatcctg tgcaactgac ggtacctgca gaataagcac cggctaacta 480 cgtgccagca gccgcggtaa tacgtagggt gcaagcgtta atcggaatta ctgggcgtaa 540 agcgtgcgca ggcggttcgg aaagaaagat gtgaaatccc agggcttaac cttggaactg 600 catttttaac taccgggcta gagtgtgtca gagggaggtg gaattccgcg tgtagcagtg 660 aaatgcgtag atatgcggag gaacaccgat ggcgaaggca gcctcctggg ataacactga 720 cgctcatgca cgaaagcgtg gggagcaaac aggattagat accctggtag tccacgccct 780 aaacgatgtc aactagctgt tggggccttc gggccttggt agcgcagcta acgcgtgaag 840 ttgaccgcct ggggagtacg gtcgcaagat taaaactcaa aggaattgac ggggacccgc 900 acaagcggtg gatgatgtgg attaattcga tgcaacgcga aaaaccttac ctacccttga 960 catgtctgga atcccgaaga gatttgggag tgctcgcaag agaaccggaa cacaggtgct 1020 gcatggctgt cgtcagctcg tgtcgtgaga tgttgggtta agtcccgcaa cgagcgcaac 1080 ccttgtcatt agttgctacg aaagggcact ctaatgagac tgccggttac aaaccggagg 1140 aaggtgggga tgacgtcaag tcctcatggc ccttatgggt agggcttcac acgtcataca 1200 atggtcggga cagagggtcg ccaacccgcg agggggagcc aatcccagaa acccgatcgt 1260 agtccggatc gcagtctgca actcgactgc gtgaagtcgg aatcgctagt aatcgcggat 1320 cagcatgtcg cggtgaatac gttcccgggt cttgtacaca ccgcccgtca caccatggga 1380 gtgggtttta ccagaagtag ttagcctaac cgcaaggggg gggcgattac cacggtagga 1440 ttcatgactg gggtgaagtc gtaacaaggt agccgtatcg gaagg 1485 40 1464 DNA Bordetella pertussis modified_base (87)..(1391) N = A, C, G or T/U 40 aactgaagag tttgatcctg gctcagattg aacgctggcg ggatgcttta cacatgcaag 60 tcggacggca gcacgggctt cggcctngtg gcgagtggcg aacgggtgag taatgtatcg 120 gaacgtgccc agtagcgggg gataactacg cgaaagcgta gctaataccg catacgccct 180 acgggggaaa gcgggggacc ttcgggcctc gcactattgg agcggccgat atcggattag 240 ctngttggtg gggtaacggc ctaccaaggc gacgatccgt agctggtttg agaggacgac 300 cagccacact gggactgaga cacggcccag nctcctacgg gaggcagcag tggggaattt 360 tggacaatgg gggcaaccct gatccagcca tcccgcgtgt gcgatgaagg ccttcgggtt 420 gtaaagcact tttggcagga aagaaacggc acgggctaat atcctgtgca actgacggta 480 cctgcagaat aagcaccggc taactacgtg ccagcagccg cggtaatacg tagggtgcaa 540 gcgttaatcg gaattactgg gcgtaaagcg tgcgcaggcg gttcggaaag aaagatgtga 600 aatcccaggg cttaaccttg gaactgcatt tttaactacc gggctagagt gtgtcagagg 660 gaggtggaat tccgcgtgta gcagtgaaat gcgtagatat gcggaggaac accgatggcg 720 aaggcagcct cctgggataa cactgacgct catgcacgaa agtgtgggga gcaaacagga 780 ttagataccc tggtagtcca cgccctaaac gatgtcaact agctgttggg gccttcgggc 840 cttggtagcg cagctaacgc gtgaagttga ccgcctgggg agtacggtcg caagattaaa 900 actcaaagga attgacgggg acccgcacaa gcggtggatg atgtggatta attcgatgca 960 acgcgaaaaa ccttacctac ccttgacatg tctggaatcc cgaagagatt tgggagtgct 1020 cgcaagagaa ccggaacaca ggtgctgcat ggctgtcgtc agctcgtgtc gtgagatgtt 1080 gggttaagtc ccgcaacgag cgcaaccctt gtcattagtt gctacgaaag ggcactctaa 1140 tgagactgcc ggtgacaaac cggaggaagg tggggatgac gtgaagtcct catggccctt 1200 atgggtaggg cttcacacgt catacaatgg tcgggacaga gggttgncaa cccgcgaggg 1260 ggagccaatc ccagaaaccc ggtcgtngtc cggatcgcag tctgcaactc gactgcgtga 1320 agtcggaatc gctagtaatc gcggatcagc atgtcgcggt gaatacgttc ccgggtcttg 1380 tacacaccgc ncgtcacacc atgggagtgg gttttaccag aagtagttag cctaaccgca 1440 aggggggcga ttaccacggt agga 1464 41 1535 DNA Burkholderia cepacia 41 taaactgaag agtttgatcc tggctcagat tgaacgctgg cggcatgctt aacacatgca 60 agtcgaacgg cagcacgggt gcttgcacct ggtggcgagt ggcgaacggg tgagtaatac 120 atcggaacat gtcctgtagt gggggatagc ccggcgaaag ccggattaat accgcatacg 180 atctacggat gaaagcgggg gaccttcggg cctcgcgcta tagggttggc gatggctgat 240 tagctagttg gtggggtaaa ggcctaccaa ggcgacgatc agtagctggt ctgagaggac 300 gaccagccac actgggactg agacacggcc cagactccta cgggaggcag cagtggggaa 360 ttttggacaa tgggcgaaag cctgatccag caatgccgcg tgtgtgaaga aggccttcgg 420 gttgtaaagc acttttgtcc ggaaagaaat ccctggctct aatacagtcg ggggatgacg 480 gtaccggaag aataagcacc ggctaactac gtgccagcag ccgcggtaat acgtagggtg 540 caagcgttaa tcggaattac tgggcgtaaa gcgtgcgcag gcggtttgct aagaccgatg 600 tgaaatcccc gggctcaacc tgggaactgc attggtgact ggcaggctag agtatggcag 660 aggggggtag aattccacgt gtagcagtga aatgcgtaga gatgtggagg aataccgatg 720 gcgaaggcag ccccctgggc caatactgac gctcatgcac gaaagcgtgg ggagcaaaca 780 ggattagata ccctggtagt ccacgcccta aacgatgtca actagttgtt ggggattcat 840 ttccttagta acgtagctaa cgcgtgaagt tgaccgcctg gggagtacgg tcgcaagatt 900 aaaactcaaa ggaattgacg gggacccgca caagcggtgg atgatgtgga ttaattcgat 960 gcaacgcgaa aaaccttacc tacccttgac atggtcggaa tcctgctgag aggtgggagt 1020 gctcgaaaga gaaccggcgc acaggtgctg catggctgtc gtcagctcgt gtcgtgagat 1080 gttgggttaa gtcccgcaac gagcgcaacc cttgtcctta gttgctacgc aagagcactc 1140 taaggagact gccggtgaca aaccggagga aggtggggat gacgtcaagt cctcatggcc 1200 cttatgggta gggcttcaca cgtcatacaa tggtcggaac agagggttgc caacccgcga 1260 gggggagcta atcccagaaa acccatcgta gtccggattg cactctgcaa ctcgagtgca 1320 tgaagctgga atcgctagta atcgcggatc agcatgccgc ggtgaatacg ttcccgggtc 1380 ttgtacacac cgcccgtcac accatgggag tgggttttac cagaagtggc tagtctaacc 1440 gcaaggagga cggtcaccac ggtaggattc atgactgggg tgaagtcgta acaaggtagc 1500 cgtatcggaa ggtgcggctg gatcacctcc tttct 1535 42 1488 DNA Burkholderia mallei 42 agattgaacg ctggcggcat gccttacaca tgcaagtcga acggcagcac gggcttcggc 60 ctggtggcga gtggtgaacg ggtgagtaat acatcggaac atgtcctgta gtgggggata 120 gcccggcgaa agccggatta ataccgcata cgatctgagg atgaaagcgg gggaccttcg 180 ggcctcgcgc tatagggttg gccgatggct gattagctag ttggtggggt aaaggcctac 240 caaggcgacg atcagtagct ggtctgagag gacgaccagc cacactggga ctgagacacg 300 gcccagactc ctacgggagg cagcagtggg gaattttgga caatgggcgc aagcctgatc 360 cagcaatgcc gcgtgtgtga agaaggcctt cgggttgtaa agcacttttg tccggaaaga 420 aatcattctg gctaataccc ggagtggatg acggtaccgg aagaataagc accggctaac 480 tacgtgccag cagccgcggt aatacgtagg gtgcgagcgt taattggaat tactgggcgt 540 aaagcgtgcg caggcggttt gctaagaccg atgtgaaatc cccgggctca acctgggaac 600 tgcattggtg actggcaggc tagagtatgg cagagggggg tagaattcca cgtgtagcag 660 tgaaatgcgt agagatgtgg aggaataccg atggcgaagg cagccccctg ggccaatact 720 gacgctcatg cacgaaagcg tggggagcaa acaggattag ataccctggt agtccacgcc 780 ctaaacgatg tcaactagtt gttggggatt catttcctta gtaacgtagc taacgcgtga 840 agttgaccgc ctggggagta cggtcgcaag attaaaactc aaaggaattg acggggaccc 900 gcacaagcgg tggatgatgt ggattaattc gatgcaacgc gaaaaacctt acctaccctt 960 gacatggtcg gaagcccgat gagagttggg cgtgctcgaa agagaaccgg cgcacaggtg 1020 ctgcatggct gtcgtcagct cgtgtcgtga gatgttgggt taagtcccgc aacgagcgca 1080 acccttgtcc ttagttgcta cgcaagagca ctctaaggag actgccggtg acaaaccgga 1140 ggaaggtggg gatgacgtca agtcctcatg gcccttatgg gtagggcttc acacgtcata 1200 caatggtcgg aacagagggt cgccaacccg cgagggggag ccaatcccag aaaaccgatc 1260 gtagtccgga ttgcactctg caactcgagt gcatgaagct ggaatcgcta gtaatcgcgg 1320 atcagcatgc cgcggtgaat acgttcccgg gtcttgtaca caccgcccgt cacaccatgg 1380 gagtgggttt taccagaagt ggctagtcta accgcaagga ggacggtcac cacggtagga 1440 ttcatgactg gggtgaagtc gtaacaaggt agccgtatcg gaaggtgc 1488 43 1610 DNA Burkholderia pseudomallei 43 tctagatgcg tgctcgagcg gccgcccagt gctgcatgga tatctgctga attcggcttg 60 agcagtttga tcctggctca gattgaacgc tggcggcatg ccttacacat gcaagtcgaa 120 cggcagcacg ggcttcggcc tggtggcgag tggcgaacgg gtgagttata catcggagca 180 tgtcctgtag tgggggatag cccggcgaaa gccgaattaa taccgcatac gatctgagga 240 tgaaagcggg ggaccttcgg gcctcgcgct atagggttgg ccgatggctg attagctagt 300 tggtggggta aaggcctacc aaggcgacga tcagtagctg gtctgagagg acgaccagcc 360 acactgggac tgagacacgg cccagactcc tacgggaggc agcagtgggg aattttggac 420 aatgggcgca agcctgatcc agcaatgccg cgtgtgtgaa gaaggccttc gggttgtaaa 480 gcacttttgt ccggaaagaa atcattctgg ctaatacccg gagtggatga cggtaccgga 540 agaataagca ccggctaact acgtgccagc agccgcggta atacgtaggg tgcgagcgtt 600 aatcgggatt actgggcgta aagcgtgcgc aggcggtttg ctaagaccga tgtgaaatcc 660 ccgggctcaa cctgggaact gcattggtga ctggcaggct agagtatggc agaggggggt 720 agaattccac gtgtagcagt gaaatgcgta gagatgtgga ggaataccga tggcgaaggc 780 agccccctgg gccaatactg acgctcatgc acgaaagcgt ggggagaaaa caggattaga 840 taccctggta gtccacgccc taaacgatgt caactagttg ttggggattc atttccttag 900 taacgtagct aacgcgcgaa gttgaccgcc tggggagtac ggtcgcaaga ttaaaactca 960 aaggaattga cggggacccg cacaagcggt ggatgatgtg gattaattcg atgcaacgcg 1020 aaaaacctta cctacccttg acatggtcgg aagcccgatg agagttgggc gtgctcgaaa 1080 gagaaccggc gcacaggtgc tgcatggctg tcgtcagctc gtgtcgtgag atgttgggtt 1140 aagtcccgca acgagcgcaa cccttgtcct tagttgctac gcaagagcac tctaaggaga 1200 ctgccggtga caaaccggag gaaggtgggg atgacgtcaa gtcctcatgg cccttatggg 1260 tagggcttca cacgtcatac aatggtcgga acagagggtc gccaacccgc gagggggagc 1320 caatcccaga aaaccgatcg tagtccggat tgcactctgc aactcgagtg catgaagctg 1380 gaatcgctag taatcgcgga tcagcatgcc gcggtgaata cgttcccggg tcttgtacac 1440 accgcccgtc acaccatggg agtgggtttt accagaagtg gctagtctaa ccgcaaggag 1500 gacggtcacc acggtaggat tcatgactgg ggtgaagtcg taacaaggta gccgtagaag 1560 ccgaattcca gcacactggc ggccgttact actggatccg agctcgtacc 1610 44 1544 DNA Neisseria gonorrhoeae 44 tgaacataag agtttgatcc tggctcagat tgaacgctgg cggcatgctt tacacatgca 60 agtcggacgg cagcacaggg aagcttgctt ctcgggtggc gagtggcgaa cgggtgagta 120 acatatcgga acgtaccggg tagcggggga taactgatcg aaagatcagc taataccgca 180 tacgtcttga gagggaaagc aggggacctt cgggccttgc gctatccgag cggccgatat 240 ctgattagct ggttggcggg gtaaaggccc accaaggcga cgatcagtag cgggtctgag 300 aggatgatcc gccacactgg gactgagaca cggcccagac tcctacggga ggcagcagtg 360 gggaattttg gacaatgggc gcaagcctga tccagccatg ccgcgtgtct gaagaaggcc 420 ttcgggttgt aaaggacttt tgtcagggaa gaaaaggctg ttgccaatat cggcggccga 480 tgacggtacc tgaagaataa gcaccggcta actacgtgcc agcagccgcg gtaatacgta 540 gggtgcgagc gttaatcgga attactgggc gtaaagcggg cgcagacggt tacttaagca 600 ggatgtgaaa tccccgggct caacccggga actgcgttct gaactgggtg actcgagtgt 660 gtcagaggga ggtggaattc cacgtgtagc agtgaaatgc gtagagatgt ggaggaatac 720 cgatggcgaa ggcagcctcc tgggataaca ctgacgttca tgtccgaaag cgtgggtagc 780 aaacaggatt agataccctg gtagtccacg ccctaaacga tgtcaattag ctgttgggca 840 acttgattgc ttggtagcgt agctaacgcg tgaaattgac cgcctgggga gtacggtcgc 900 aagattaaaa ctcaaaggaa ttgacgggga cccgcacaag cggtggatga tgtggattaa 960 ttcgatgcaa cgcgaagaac cttacctggt tttgacatgt gcggaatcct ccggagacgg 1020 aggagtgcct tcgggagccg taacacaggt gctgcatggc tgtcgtcagc tcgtgtcgtg 1080 agatgttggg ttaagtcccg caacgagcgc aacccttgtc attagttgcc atcattcggt 1140 tgggcactct aatgagactg ccggtgacaa gccggaggaa ggtggggatg acgtcaagtc 1200 ctcatggccc ttatgaccag ggcttcacac gtcatacaat ggtcggtaca gagggtagcc 1260 aagccgcgag gcggagccaa tctcacaaaa ccgatcgtag tccggattgc actctgcaac 1320 tcgagtgcat gaagtcggaa tcgctagtaa tcgcaggtca gcatactgcg gtgaatacgt 1380 tcccgggtct tgtacacacc gcccgtcaca ccatgggagt gggggatacc agaagtaggt 1440 agggtaaccg caaggagtcc gcttaccacg gtatgcttca tgactggggt gaagtcgtaa 1500 caaggtagcc gtaggggaac ctgcggctgg atcacctcct ttct 1544 45 1544 DNA Neisseria meningitidis 45 tgaacataag agtttgatcc tggctcagat tgaacgctgg cggcatgctt tacacatgca 60 agtcggacgg cagcacagag aagcttgctt ctcgggtggc gagtggcgaa cgggtgagta 120 acatatcgga acgtaccgag tagtggggga taactgatcg aaagatcagc taataccgca 180 tacgtcttga gagagaaagc aggggacctt cgggccttgc gctattcgag cggccgatat 240 ctgattagct agttggtggg gtaaaggcct accaaggcga cgatcagtag cgggtctgag 300 aggatgatcc gccacactgg gactgagaca cggcccagac tcctacggga ggcagcagtg 360 gggaattttg gacaatgggc gcaagcctga tccagccatg ccgcgtgtct gaagaaggcc 420 ttcgggttgt aaaggacttt tgtcagggaa gaaaaggctg ttgctaatat cagcggctga 480 tgacggtacc tgaagaataa gcaccggcta actacgtgcc agcagccgcg gtaatacgta 540 gggtgcgagc gttaatcgga attactgggc gtaaagcggg cgcagacggt tacttaagca 600 ggatgtgaaa tccccgggct caacccggga actgcgttct gaactgggtg actcgagtgt 660 gtcagaggga ggtagaattc cacgtgtagc agtgaaatgc gtagagatgt ggaggaatac 720 cgatggcgaa ggcagcctcc tgggacaaca ctgacgttca tgcccgaaag cgtgggtagc 780 aaacaggatt agataccctg gtagtccacg ccctaaacga tgtcaattag ctgttgggca 840 acctgattgc ttggtagcgt agctaacgcg tgaaattgac cgcctgggga gtacggtcgc 900 aagattaaaa ctcaaaggaa ttgacgggga cccgcacaag cggtggatga tgtggattaa 960 ttcgatgcaa cgcgaagaac cttacctggt cttgacatgt acggaatcct ccggagacgg 1020 aggagtgcct tcgggagccg taacacaggt gctgcatggc tgtcgtcagc tcgtgtcgtg 1080 agatgttggg ttaagtcccg caacgagcgc aacccttgtc attagttgcc atcattcagt 1140 tgggcactct aatgagactg ccggtgacaa gccggaggaa ggtggggatg acgtcaagtc 1200 ctcatggccc ttatgaccag ggcttcacac gtcatacaat ggtcggtaca gagggtagcc 1260 aagccgcgag gcggagccaa tctcacaaaa ccgatcgtag tccggattgc actctgcaac 1320 tcgagtgcat gaagtcggaa tcgctagtaa tcgcaggtca gcatactgcg gtgaatacgt 1380 tcccgggtct tgtacacacc gcccgtcaca ccatgggagt gggggatacc agaagtaggt 1440 aggataacca caaggagtcc gcttaccacg gtatgcttca tgactggggt gaagtcgtaa 1500 caaggtagcc gtaggggaac ctgcggctgg atcacctcct ttct 1544 46 1537 DNA Pseudomonas aeruginosa 46 gaactgaaga gtttgatcat ggctcagatt gaacgctggc agcaggggcc ttcaacacat 60 gcaagtcgag cttatgaagg gagcttgcct tggattcagc ggcggacggg tgagtaatgc 120 ctaggaatct gcctggtagt gggggataac gtccggaaac ggccgctaat accgcatacg 180 tcctgaggga gaaagtcggg gatcttcgga cctcacgcta tcagatgagc ctaggtcgga 240 ttagctagtt ggtggggtaa aggcctacca aggcgacgat ccgtaactgg tctgagagga 300 tgatcagtca cactggaact gagacacggt ccagactcct acgggaggca gcagtgggga 360 atattggaca atgggcgcaa gcctgatcca gccatgccgc gtgtgtgaag aaggtcttcg 420 gattgtaaag cactttaagt tgggaggaag ggcagtaagt taataccttg ctgtttgacg 480 ttaccaacag aataagcacc ggctaacttc gtgccagcag ccgcggtaat acgaagggtg 540 caagcgttaa tcggaattac tgggcgtaaa gcgcgcgtaa gtggttcagc aagcttgatg 600 tgaaatcccc gggctcaacc tgggaactgc atccaaaagc tactgagcta gagtacggta 660 gaggtggtag aatttcctgt gtagcggtga aatgcgtaga tataggaagg aacaccagtg 720 gcgaaggcga ccacctggac tgtactgaca ctgaggtgcg aaagcgtggg gagcaaacag 780 gattagatac cctggtagtc cacgccgtaa acgatgtcga ctagccgttg ggatccttga 840 gatcttagtg gcgcacgtaa cgcgataagt cgaccgcctg gggagtacgg ccgcaaggtt 900 aaaactcaaa tgaattgacg ggggcccgca caagcggtgg agcatgtggt ttaattcgaa 960 gcaacgcgaa gaaccttacc tggccttgac atgctgagaa ctttccagag atggattggt 1020 gccttcggga acagagacac aggtgctgca tggctgtcgt cagctcgtgt cgtgagatgt 1080 tgggttaagt cccgtaacga gcgcaaccct tgtccttagt taccagcacc tcgggtgggc 1140 actctaagga gactgccggt gacaaaccgg aggaaggtgg ggatgacgtc aagtcatcat 1200 ggcccttacg gccagggcta cacacgtgct acaatggtcg gtacaaaggg ttgccaagcc 1260 gcgagtggga gctaatccca taaaaccgat cgtagtccgg atcgcagtct gcaactcgac 1320 tgcgtgaagt cggaatcgct agtaatcgtg aatcagaatg tcacggtgaa tacgtccccg 1380 ggccttgtac acaccgcccg tcacaccatg ggagtgggtt gctccagaag tagctagtct 1440 aaccgcaagg gggacggtta ccacggagtg attcatgact ggggtgaagt cgtaacaagg 1500 tagccgtagg ggaacctgcg gctggatcac ctcctta 1537 47 1467 DNA Vibrio cholerae modified_base (928)..(1464) N = A, C, G or T/U 47 attgaagagt ttgatcctgg ctcagattga acgctggcgg caggcctaac acatgcaagt 60 cgagcggcag cacagaggaa cttgttcctt gggtggcgag cggcggacgg gtgagtaatg 120 cctgggaaat tgcccggtag agggggataa ccattggaaa cgatggctaa taccgcataa 180 cctcgcaaga gcaaagcagg ggaccttcgg gccttgcgct accggatatg cccaggtggg 240 attagctagt tggtgaggta agggctcacc aaggcgacga tccctagctg gtctgagagg 300 atgatcagcc acactggaac tgagacacgg tccagactcc tacgggaggc agcagtgggg 360 aatattgcac aatgggcgca agcctgatgc agccatgccg cgtgtatgaa gaaggccttc 420 gggttgtaaa gtactttcag tagggaggaa ggtggttaag ttaatacctt aatcatttga 480 cgttacctac agaagaagca ccggctaact ccgtgccagc agccgcggta atacggaggg 540 tgcaagcgtt aatcggaatt actgggcgta aagcgcatgc aggtggtttg ttaagtcaga 600 tgtgaaagcc ctgggctcaa cctaggaatc gcatttgaaa ctgacaagct agagtactgt 660 agaggggggt agaatttcag gtgtagcggt gaaatgcgta gagatctgaa ggaataccgg 720 tggcgaaggc ggccccctgg acagatactg acactcagat gcgaaagcgt ggggagcaaa 780 caggattaga taccctggta gtccacgccg taaacgatgt ctacttggag gttgtgccct 840 agagtcgtgg ctttcggagc taacgcgtta agtagaccgc ctggggagta cggtcgcaag 900 attaaaactc aaatgaattg acgggggncc gcacaagcgg tggagcatgt ggtttaattc 960 ganncaacgc gaagaacctt acctactctt gacatccaga gaatctagcg gagacgctgg 1020 agtgccttcg ggagctctga gacaggtgct gcatggctgt cgtcagctcg tgttgtgaaa 1080 tgttgggtta agtcccgcaa cgagcgcaac ccttatcctt gtttgccagc acgtaatggt 1140 gggaactcca gggagactgc cggtgataaa ccggaggaag gtggggacga cgtcaagtca 1200 tcatggccct tacgagtagg gctacacacg tgctacaatg gcgtatacag agggcagcga 1260 taccgcgagg tggagcgaat ctcacaaagt acgtcgtagt ccggattgga gtctgcaact 1320 cgactccatg aagtcggaat cgctagtaat cgcaaatcag aatgttgcgg tgaatacgtt 1380 cccgggcctt gtacacaccg cccgtcacac catgggagtg ggctgcaaaa gaagcangta 1440 gtttaacctt cgggaggacg cttnccc 1467 48 1485 DNA Yersinia enterocolitica modified_base (1)..(1484) N = A, C, G or T/U 48 naattgaaga gtttgatcat ggctcagatn gaacgctggc ggcaggccta acacatgcaa 60 gtcgagcggc agcgggaagn agtttactac tttcngggcg agcggcgnac gggtgagtaa 120 tgtctgggaa actgcctgat ggagggggat aactactgga aacggtagct aataccgcat 180 aacgtcttcg gaccaaagtg ggggacctta gggcctcacg ccatcngatg tgcccagatg 240 ggattagcta gtaggtgggg taatggctca cctaggcgac gatccctagc tggtctgaga 300 ggatgaccag ccacactgga actgagacac ggtccagact cctacgggag gcagcagtgg 360 ggaatattgc acaatgggcg caagcctgat gcagccatgc cgcgtgtgtg aagaaggcct 420 tcgggttgta aagcactttc agcgaggagg aaggccaata acttaatacg ttgttggatt 480 gacgttactc gcagaagaag caccggctaa ctccgtgcca gcagccgcgg taatacggag 540 ggtgcaagcg ttaatcggaa ttactgggcg taaagcgcac gcaggcggtt tgttaagtca 600 gatgtgaaat ccccgcgctt aacgtgggna cngcatttga aactggcaag ctagagtctt 660 gtagaggggg gtagaattcc aggtgtagcg gtgaaatgcg tagagatctg naggaatacc 720 ggtggcgaag gcggccccct ggacaaagac tgacgctcag gtgcgaaagc gtggggagca 780 aacaggatta gataccctgg tagtccacgc tgtaaacgat gtcgacttgg aggttgtgcc 840 cttgaggcgt ggcttccgga gctaacgcgt taagtcgacc gcctggggag tacggccgca 900 aggttaaaac tcaaatgaat tnncgggggc cngcacaagc ggtggagcat gtggtttaat 960 tcgatgcaac gcgaagaacc ttacctactc ttgacatcca cggaatttag cagagatgct 1020 ttagtgnctt cgggaaccgt gagacaggtg ctgcatggct gtcgtcagct cgtgttgtga 1080 aatgttgggt taagtcccgc aacgagcgca acccttatcc tttgttgcca gcacgtaatg 1140 gtgggaactc aaaggagact gccggtgata aaccggagga aggtggggat gacgtcaagt 1200 catcatggcc cttacgagta gggctacaca cgtgctacaa tggcagatac aaagtgaagc 1260 gaactcgcga gagcaagcgg accacataaa gtctgtcgta gtccggattg gagtctgcaa 1320 ctcgactcca tgaagtcgga atcgctagta atcgtagatc agaatgctac ggtgaatacg 1380 ttcccgggcc ttgtacacac cgcccgtcac accntgggag tgggttgcaa aagaagtagg 1440 tagcttaacn ttcgggaggg cgcgtaccac tttgtgattc nngnc 1485 49 2927 DNA Bacillus subtilis 49 ggttaagtta gaaagggcgc acggtggatg ccttggcact aggagccgat gaaggacggg 60 acgaacaccg atatgcttcg gggagctgta agcaagcttt gatccggaga tttccgaatg 120 gggaaaccca ccactcgtaa tggagtggta tccatatctg aattcatagg atatgagaag 180 gcagacccgg ggaactgaaa catctaagta cccggagaag agaaagcaaa tgcgattccc 240 tgagtagcgg cgacgaacac gggatcagcc caaaccaaga ggcttgcctc tgtggttgta 300 ggacactctg tacggagtta caaaagaacg aggtagatga agaggtctgg aaagggcccg 360 ccataggagg taacagccct gtagtcaaaa cttcgttctc tcctgagtgg atcctgagta 420 cggcggaaca cgtgaaattc cgtcggaatc cgggaggacc atctcccaag gctaaatact 480 ccctagtgac cgatagtgaa ccagtaccgt gagggaaagg tgaaaagcac cccggaaggg 540 gagtgaaaga gatcctgaaa ccgtgtgcct acaagtagtc agagcccgtt aacggtgatg 600 gcgtgccttt tgtagaatga accggcgagt tacgatcccg tgcaaggtta agcagaagat 660 gcggagccgc agcgaaagcg agtctgaata gggcgcatga gtacgtggtc gtagacccga 720 aaccaggtga tctacccatg tccagggtga agttcaggta acactgaatg gaggcccgaa 780 cccacgcacg ttgaaaagtg cggggatgag gtgtgggtag gggtgaaatg ccaatcgaac 840 ctggagatag ctggttctct ccgaaatagc tttagggcta gcctcaaggt aagagtcttg 900 gaggtagagc actgattgga ctaggggccc tcaccgggtt accgaattca gtcaaactcc 960 gaatgccaat gacttatcct tgggagtcag actgcgagtg ataagatccg tagtcgaaag 1020 ggaaacagcc cagaccgcca gctaaggtcc caaagtatac gttaagtgga aaaggatgtg 1080 gagttgctta gacaaccagg atgttggctt agaagcagcc accatttaaa gagtgcgtaa 1140 tagctcactg gtcgagtgac tctgcgccga aaatgtaccg gggctaaacg tatcaccgaa 1200 gctgcggact gttcttcgaa cagtggtagg agagcgttct aagggctgtg aagccagacc 1260 ggaaggactg gtggacggct tagaagtgag aatgccggta tgagtagcga aaagaggggt 1320 gagaatccct ccaccgaatg cctaagggtt cctgaggaag gctcgtccgc tcagggttag 1380 tcgggaccta agccgaggcc gaaaggcgta ggcgatggac aacaggttga tattcctgta 1440 ccacctcctc accatttgag caatgggggg tcgcaggagg atagggtaag cgcggtattg 1500 gatatccgcg tccaagcagt taggctggga aataggcaaa tccgtttccc ataaggctga 1560 gctgtgatgg cgagcgaaat atagtagcga agttcctgat tccacactgc caagaaaagc 1620 ctctagcgag gtgagaggtg cccgtaccgc aaaccgtcac aggtaggcga ggagagaatc 1680 ctaaggtgat cgagagaact ctcgttaagg aactcggcaa aatgaccccg taacttcggg 1740 agaaggggtg ctctgttagg gtgcaagccc gagagagccg cagtgaatag gcccaggcga 1800 ctgtttagca aaaacacagg tctctgcgaa gccgtaaggc gaagtatagg ggctgacgcc 1860 tgcccggtgc tggaaggtta agaggagcgc ttagcgtaag cgaaggtgcg aattgaagcc 1920 ccagtaaacg gcggccgtaa ctataacggt cctaaggtag cgaaattcct tgtcgggtaa 1980 gttccgaccc gcacgaaagg cgcaacgatc tgggcgctgt ctcaacgaga gactcggtga 2040 aattatagta cctgtgaaga tgcaggttac ccgcgacagg acggaaagac cccgtggagc 2100 tttactgcag cctgatattg aatgttggta cagcttgtac aggataggta ggagccttgg 2160 aaaccggagc gccagcttcg gtggaggcat cggtgggata ctaccctggc tgtattgacc 2220 ttctaacccc ccgcccttat cgggcgggga gacagtgtca ggtgggcagt ttgactgggg 2280 cggtcgcctc ctaaaaggta acggaggcgc ccaaaggttc cctcagaatg gttggaaatc 2340 attcgcagag tgtaaaggca caagggagct tgactgcgag acctacaagt cgagcaggga 2400 cgaaagtcgg gcttagtgat ccggtggttc cgcatggaag ggccatcgct caacggataa 2460 aagctacccc ggggataaca ggcttatctc ccccaagagc tccacatcga cggggaggtt 2520 tggcacctcg atgtcggctc atcgcatcct ggggctgtag tcggtcccaa gggttgggct 2580 gttcgcccat taaagcggta cgcgagctgg gttcagaacg tcgtgagaca gttcggtccc 2640 tatccgtcgc gggcgctgga aatttgagag gagctgtcct tagtacgaga ggaccgggat 2700 ggacgcaccg ctggtgtacc agttgttctg ccaagggcat cgctgggtag ctatgtgcgg 2760 acgggataag tgctgaaagc atctaagcat gaagcccccc tcaagatgag atttcccatt 2820 ccgcaaggaa gtaagatccc tgaaagatga tcaggttgat aggtctgagg tggaagtgtg 2880 gcaacacatg gagctgacag atactaatcg atcgaggact taaccat 2927 50 2922 DNA Bacillus anthracis 50 ggttaagtta gaaagggcgc acggtggatg ccttgacact aggagtcgat gaaggacggg 60 actaacgccg atatgcttcg gggagctgta agtaagcttt gatccgaaga tttccgaatg 120 gggaaaccca ccatacgtaa tggtatggta tccttatctg aatacatagg gtaaggaaga 180 cagacccagg gaactgaaac atctaagtac ctggaggaag agaaagcaaa tgcgatttcc 240 tgagtagcgg cgagcgaaac ggaacatagc ccaaaccaag aggcttgcct cttggggttg 300 taggacattc tatacggagt tacaaaggaa cgaggtagac gaagcgacct ggaaaggtcc 360 gtcgtagagg gtaacaaccc cgtagtcgaa acttcgttct ctcttgaatg tatcctgagt 420 acggcggaac acgtgaaatt ccgtcggaat ctgggaggac catctcccaa ggctaaatac 480 tccctagtga tcgatagtga accagtaccg tgagggaaag gtgaaaagca ccccggaagg 540 ggagtgaaag agatcctgaa accgtgtgcc tacaaatagt cagagcccgt taacgggtga 600 tggcgtgcct tttgtagaat gaaccggcga gttacgatcc cgtgcgaggt taagctgaag 660 aggcggagcc gcagcgaaag cgagtctgaa tagggcgttt agtacgtggt cgtagacccg 720 aaaccaggtg atctacccat gtccagggtg aagttcaggt aacactgaat ggaggcccga 780 acccacgcac gttgaaaagt gcggggatga ggtgtgggta gcggagaaat tccaatcgaa 840 cctggagata gctggttctc cccgaaatag ctttagggct agccttaagt gtaagagtct 900 tggaggtaga gcactgattg gactaggggt cctcatcgga ttaccgaatt cagtcaaact 960 ccgaatgcca atgacttatc cttaggagtc agactgcgag tgataagatc cgtagtcaaa 1020 agggaaacag cccagaccgc cagctaaggt cccaaagtgt gtattaagtg gaaaaggatg 1080 tggagttgct tagacaacta ggatgttggc ttagaagcag ccaccattta aagagtgcgt 1140 aatagctcac tagtcgagtg actctgcgcc gaaaatgtac cggggctaaa tacaccaccg 1200 aagctgcgga ttgataccaa tggtatcagt ggtaggggag cgttctaagg acagtgaagt 1260 cagaccggaa ggactggtgg agtgcttaga agtgagaatg ccggtatgag tagcgaaaga 1320 cgggtgagaa tcccgtccac cgaatgccta aggtttcctg aggaaggctc gtccgctcag 1380 ggttagtcag gacctaagcc gaggccgaca ggcgtaggcg atggacaaca ggttgatatt 1440 cctgtaccac ctctttatcg tttgagcaat ggagggacgc agaaggatag aagaagcgtg 1500 cgattggttg tgcacgtcca agcagttagg ctgataagta ggcaaatccg cttatcgtga 1560 aggctgagct gtgatgggga agctccttat ggagcgaagt ctttgattcc ccgctgccaa 1620 gaaaagcttc tagcgagata aaaggtgcct gtaccgcaaa ccgacacagg taggcgagga 1680 gagaatccta aggtgtgcga gagaactctg gttaaggaac tcggcaaaat gaccccgtaa 1740 cttcgggaga aggggtgctt tcttaacgga aagccgcagt gaataggccc aagcgactgt 1800 ttagcaaaaa cacagctctc tgcgaagccg taaggcgaag tatagggggt gacacctgcc 1860 cggtgctgga aggttaagga gaggggttag cgtaagcgaa gctctgaact gaagccccag 1920 taaacggcgg ccgtaactat aacggtccta aggtagcgaa attccttgtc gggtaagttc 1980 cgacccgcac gaaaggtgta acgatttggg cactgtctca accagagact cggtgaaatt 2040 atagtacctg tgaagatgca ggttacccgc gacaggacgg aaagaccccg tggagcttta 2100 ctgtagcctg atattgaatt ttggtacagt ttgtacagga taggcgggag cctttgaaac 2160 cggagcgcta gcttcggtgg aggcgctggt gggataccgc cctgactgta ttgaaattct 2220 aacctacggg tcttatcgac ccgggagaca gtgtcaggtg ggcagtttga ctggggcggt 2280 cgcctcctaa agtgtaacgg aggcgcccaa aggttccctc agaatggttg gaaatcattc 2340 gtagagtgca aaggcataag ggagcttgac tgcgagacct acaagtcgag cagggacgaa 2400 agtcgggctt agtgatccgg tggttccgca tggaagggcc atcgctcaac ggataaaagc 2460 taccccgggg ataacaggct tatctccccc aagagtccac atcgacgggg aggtttggca 2520 cctcgatgtc ggctcatcgc atcctggggc tgtagtcggt cccaagggtt gggctgttcg 2580 cccattaaag cggtacgcga gctgggttca gaacgtcgtg agacagttcg gtccctatcc 2640 gtcgtgggcg taggaaattt gagaggagct gtccttagta cgagaggacc gggatggacg 2700 caccgctggt gtaccagttg ttctgccaag ggcatagctg ggtagctatg tgcggaaggg 2760 ataagtgctg aaagcatcta agcatgaagc ccccctcaag atgagatttc ccatagcgta 2820 agctagtaag atccctgaaa gatgatcagg ttgataggtt cgaggtggaa gcatggtgac 2880 atgtggagct gacgaatact aatagatcga ggacttaacc at 2922 51 2912 DNA Enterococcus faecalis 51 ggttaagtga ataagggcgc acggtggatg ccttggcact aggagccgat gaaggacggg 60 actaacaccg atatgctttg gggagctgta agtaagctat gatccagaga tttccgaatg 120 ggggaaccca atatctttta taggatatta cttttcagtg aatacatagc tgattagagg 180 tagacgcaga gaactgaaac atcttagtac ctgcaggaag agaaagaaaa ttcgattccc 240 tgagtagcgg cgagcgaaac gggaagagcc caaaccaaca agcttgcttg ttggggttgt 300 aggactccaa tatggtagtc tgttagtata gttgaaggat ttggaaaatt ccgctaaaga 360 gggtgaaagc cccgtagacg aaatgctaac aacacctagg aggatcctga gtacggcgga 420 acacgagaaa ttccgtcgga atccgcgggg accatcccgc aaggctaaat actccctagt 480 gaccgatagt gaaccagtac cgtgagggaa aggtgaaaag caccccggaa ggggagtgaa 540 atagatcctg aaaccgtgtg cctacaacaa gtcaaagctc gttaatgagt gatggcgtgc 600 cttttgtaga atgaaccggc gagttacgat tgcatgcgag gttaagtcga agagacggag 660 ccgcagcgaa agcgagtctg aatagggcga atgagtatgt agtcgtagac ccgaaaccat 720 gtgatctacc catgtccagg ttgaaggtgc ggtaaaacgc actggaggac cgaacccacg 780 tacgttgaaa agtgcgggga tgaggtgtgg gtagcggaga aattccaaac gaacttggag 840 atagctggtt ctctccgaaa tagctttagg gctagcctcg gaattgagaa tgatggaggt 900 agagcactgt ttggactagg ggcccatctc gggttaccga attcagataa actccgaatg 960 ccattcattt atatccggga gtcagactgc gagtgataag atccgtagtc gaaagggaaa 1020 cagcccagac caccagctaa ggtcccaaaa tatatgttaa gtggaaaagg atgtggggtt 1080 gcacagacaa ctaggatgtt ggcttagaag cagccaccat ttaaagagtg cgtaatagct 1140 cactagtcga gtgaccctgc gccgaaaatg taccggggct aaacatatta ccgaagctgt 1200 ggactacacc attaggtgta gtggtaggag agcgttctaa gggcgttgaa ggtcgatcgt 1260 gaggacggct ggagcgctta gaagtgagaa tgccggtatg agtagcgaaa gacaggtgag 1320 aatcctgtcc accgtatgac taaggtttcc tggggaaggc tcgtccgccc agggttagtc 1380 gggacctaag ccgaggccga taggcgtagg cgatggacaa caggttgata ttcctgtacc 1440 agttgttttt gtttgagcaa tggagggacg cagtaggcta aggaatgcat gcgattggaa 1500 gtgcatgtcc aagcaatgag tcttgagtag agttaaatgc tttactcttt aaggacaagt 1560 tgtgacgggg agcgaaataa tagtagcgaa gttcctgatg tcacactgcc aagaaaagct 1620 tctagtgaga aaacaactgc ccgtaccgta aaccgacaca ggtagtcgag gagagtatcc 1680 taaggtgagc gagcgaactc tcgttaagga actcggcaaa atgaccccgt aacttcggga 1740 gaaggggtgc tgacttcggt cagccgcagt gaataggccc aagcgactgt ttatcaaaaa 1800 cacaggtctc tgcaaaatcg taagatgaag tataggggct gacgcctgcc cggtgctgga 1860 aggttaagag gatgggttag cttcggcgaa gctcagaatt gaagccccag taaacggcgg 1920 ccgtaactat aacggtccta aggtagcgaa attccttgtc gggtaagttc cgacccgcac 1980 gaaaggcgta acgatttggg cactgtctca acgagagact cggtgaaatt ttagtacctg 2040 tgaagatgca ggttacccgc gacaggacgg aaagacccca tggagcttta ctgtagtttg 2100 atattgagtg tttgtaccac atgtacagga taggtaggag ccgatgagac cggaacgcta 2160 gtttcggagg aggcgctggt gggatactac ccttgtgtta tgaaccctct aacccgcacc 2220 actaatcgtg gtgggagaca gtgtcagatg ggcagtttga ctggggcggt cgcctcctaa 2280 aaggtaacgg aggcgcccaa aggttccctc agaatggttg gaaatcattc gaagagtgta 2340 aaggcagaag ggagcttgac tgcgagacct acaagtcgag cagggacgaa agtcgggctt 2400 agtgatccgg tggttccgca tggaagggcc atcgctcaac ggtaaaagct accctgggga 2460 taacaggctt atctccccca agagtccaca tcgacgggga ggtttggcac ctcgatgtcg 2520 gctcgtcgca tcctggggct gtagtcggtc ccaagggttg ggctgttcgc ccattaaagc 2580 ggcacgcgag ctgggttcag aacgtcgtga gacagttcgg tccctatccg tcgcgggcgt 2640 tggaaatttg agaggagctg tccttagtac gagaggaccg ggatggactt accgctggtg 2700 taccagttgt tctgccaagg gcattgctgg gtagctatgt agggaaggga taaacgctga 2760 aagcatctaa gtgtgaagcc cacctcaaga tgagatttcc catttcttta agaaagtaag 2820 acccctgaga gatgatcagg tagataggtt ggaagtggaa ggctagtgat agttggagcg 2880 gaccaatact aatcggtcga ggacttaacc aa 2912 52 2898 DNA Lactococcus lactis 52 ggcaaagtta ataagggcgc acggtggatg ccttggcact aagagccgat gaaggacgtg 60 actaacgacg atattctagg gggagcagta agtacgcatt gatccctagg tctccgaatg 120 ggaaaaccca gctgctacta gcagttattc atgagtgaat acatagctca tgtaaaggta 180 acgcagagaa ctgaaacatc taagtacctg caggaagaga aagtaaaaac gatttcgtaa 240 gtagcggcga gcgaacgcga agaagggcaa accaagaagc ttgcttcttg gggttgtagg 300 actgcaacgt ggacttaagc attatagtcg aataacctgg gaaggttaat caaagagggt 360 aataatcccg tagacgaaat agcgcttata cctagcagta tcctgagtag ggctggacac 420 gcgaaatcca gtttgaatcc gggaggacca tctcccaacc ctaaatactc cttagtgacc 480 gatagtgaac cagtaccgtg agggaaaggt gaaaagaacc cgagagggga gtgaaatagc 540 acctgaaacc gtgtgcctac aagaagttcg agcccgttaa tgggtgagag cgtgcctttt 600 gtagaatgaa ccggcgagtt acgttatgat gcgaggttaa gttgaagaga cggagccgta 660 gggaaaccga gtctgaatag ggcgacttag tatcatgatg tagacccgaa acctagtgac 720 ctatccatga gcagggtgaa ggtgtggtaa gacgcactgg aggcccgaac caggacacgt 780 tgaaaagtgt ttggatgact tgtggatagc ggagaaattc caaacgaact gggagatagc 840 tggttctctc cgaaatagct ttagggctag cgtcgaaatg taagtgtatt ggaggtagag 900 cactgtttgg gtgaggggtc cgtctaggat taccaatctc agataaactc cgaatgctaa 960 tacacatgtt cggcagtcag actgcgagtg ctaagatccg tagtcgaaag ggaaacagcc 1020 cagaccaaca gctaaggtcc caaaatatat gttaagtgga aaaggatgtg gggttgcaca 1080 gacaactagg atgttagctc agaagcagct atcattcaaa gagtgcgtaa tagctcacta 1140 gtcgagtgac cctgcgccga aaatgtaccg gggctaaaca tattaccgaa gctttggatt 1200 gatattttat caatggtagg agagcgttct taaccgcgat gaaggtatac cgtgaggagt 1260 gctggagcgt taagaagtga gaatgccggt atgagtagcg caagataagt gagaatctta 1320 tccaccgtaa gactaaggtt tccaggggaa ggctcgtccg ccctgggtta gtcgggacct 1380 aaggcgaggc cgaaaggcgt agtcgatgga caactggttg atattccagt actagatatg 1440 atcgtgatgg agggacgcag taggctaaga gatgccagtt aatggattct ggtctaagca 1500 gtgaggtgtg agatgtgtca aatgcatttc tctttaacat tgagctgtga tggggaagca 1560 actacggttg cgaactctct gatgtcacac tgccaagaaa agcttctagc gtaaagtcat 1620 atctacccgt accgcaaacc gacacaggtg gtcgaggcga gtagcctcag gtgatcgaga 1680 gaactctcgt taaggaactc ggcaaaatag ccccgtaact tcgggagaag gggtgctggt 1740 gtaaaagcca gccgcagtga ataggcccaa gcaactgttt atcaaaaaca cagctctctg 1800 ctaaaccgca aggtgatgta tagggggtga cgcctgcccg gtgctggaag gttaagagga 1860 gtgcttagac gtaagtcgaa ggtatgaatt gaagccccag taaacggcgg ccgtaactat 1920 aacggtccta aggtagcgaa attccttgtc gggtaagttc cgacccgcac gaaaggcgta 1980 atgatttggg cactgtctca acgagagact cggtgaaatt ttagtacctg tgaagatgca 2040 ggttacccgc gacaggacgg aaagacccca tggagcttta ctgtagtttg atattgagta 2100 cctgtaagtc atgtacagga taggtaggag ccattgaaat agggacgcta gtttctattg 2160 aggcgttgtt gggatactac ccttgactta tggttactct aacccgctgg cataatcggc 2220 cagggagaca gtgtctgacg gacagtttga ctggggcggt cgctcctaaa gagtaacgga 2280 ggcgctcaaa ggttggctca gattggttgg aaatcaatcg tagagtgtaa aggtaaaagc 2340 cagcttgact gcgagagcta caactcgagc aggtaggaaa ctaggactta gtgatccggt 2400 ggtaccgcat ggaagggcca tcgctcaacg gataaaagct accctgggga taacaggctt 2460 atctccccca agagttcaca tcgacgggga ggtttggcac ctcgatgtcg gctcgtcgca 2520 tcctggggct gtagtcggtc ccaagggttg ggctgttcgc cattaaagcg gcacgcgagc 2580 tgggttcaga acgtcgtgag acagttcggt ccctatccgt cgcgggcgta ggtaatttga 2640 gaggatctgt ccttagtacg agaggaccgg gatggactta ccgctggtgt accagttgtt 2700 ccgccaggag cacggctgga tagctatgta gggaagggat aagcgctgaa agcatctaag 2760 tgcgaagccc acctcaagat gagattaccc attcgtaaga attaagagcc cagagagatg 2820 atctggtaga taggctggaa gtggaagagt tgcgagactt ggagcggacc agtactaatc 2880 gctcgaggac tttaccaa 2898 53 2932 DNA Listeria monocytogenes 53 ggttaagtta gaaagggcgc acggtggatg ccttggcact aggagccgaa gaaggacggg 60 actaacaccg atatgctttg gggagctgta cgtaagcgtt gatccagaga tttccgaatg 120 ggggaaccca ctatctttag tcggatagta tccttacgtg aatacatagc gtgaggaagg 180 cagacccagg gaactgaaac atctaagtac ctggaggaag agaaagaaaa atcgatttcc 240 tgagtagcgg cgagcgaaac ggaaagagcc caaaccaaga agcttgcttc ttggggttgt 300 aggacactct atacggagtt acaaaagaaa gttataaatg aagcggtctg gaaaggcccg 360 ccaaagacgg taacagcccg gtagttgaaa tggctttccc tccagagtgg atcctgagta 420 cggcggaaca cgtgaaattc cgtcggaatc cgggaggacc atctcccaag gctaaatact 480 ccctagtgac cgatagtgaa ccagtaccgt gagggaaagg tgaaaagcac cccggaaggg 540 gagtgaaaca gttcctgaaa ccgtgtgcct acaagtagtt agagcccgtt aatgggtgat 600 agcgtgcctt ttgtagaatg aaccggcgag ttacgatttg ttgcaaggtt aagcggaaaa 660 agcggagccg tagcgaaagc gagtctgaat agggcgcata agtaacaggt cgtagacccg 720 aaaccaggtg atctacccat gtccaggatg aaggtaaggt aatacttact ggaggtccga 780 acccacgcac gttgaaaagt gcggggatga ggtgtgggta gcggagaaat tccaatcgaa 840 cttggagata gctggttctc tccgaaatag ctttagggct agcctcgagg taaagagtca 900 tggaggtaga gcactgtttg gactaggggc ccttctcggg ttaccgaatt cagataaact 960 ccgaatgcca tgtacttata ctcgggagtc agactgcgag tgataagatc cgtagtcgaa 1020 agggaaacag cccagaccac cagttaaggt ccccaaatat atgttaagtg gaaaaggatg 1080 tggggttgct tagacaacca ggatgttggc ttagaagcag ccaccattga aagagtgcgt 1140 aatagctcac tggtcgagtg accccgcgcc gaaaatgtac cggggctaaa catattaccg 1200 aaactgtgga tgaacctctt tagaggttcg tggtaggaga gcgttctaag ggcggtgaag 1260 tcagaccgga aggactggtg gagcgcttag aagtgagaat gccggtatga gtagcgaaag 1320 aagggtgaga atcccttcca ccgaatatct aaggtttcct gaggaaggct cgtccgctca 1380 gggttagtcg ggacctaagc cgaggccgat aggcgtaggc gatggacaac aggtagagat 1440 tcctgtacca gtgctaattg tttaaccgat ggggtgacac agaaggatag ggaatcgcac 1500 gaatggaaat gtgcgtccaa gcagtgagtg tgagaagtag gcaaatccgc ttctcacgaa 1560 gcatgagctg tgatggggaa ggaaattaag tacggaagtt cctgatttca cgctgtcaag 1620 aaaagcctct aggaagagta gtactgcccg taccgcaaac cgacacaggt agatgaggag 1680 agaatcctaa ggtgagcgag agaactctcg ttaaggaact cggcaaaatg accccgtaac 1740 ttcgggagaa ggggtgctct attagggtgc aagcccgaga gagccgcagt gaataggccc 1800 aggcgactgt ttagcaaaaa cacaggtctc tgcaaaaccg taaggtgacg tataggggct 1860 gacgcctgcc cggtgctgga aggttaagag gagtgcttag cttcggcgaa ggtacgaatt 1920 gaagccccag taaacggcgg ccgtaactat aacggtccta aggtagcgaa attccttgtc 1980 gggtaagttc cgacccgcac gaaaggcgca acgatctggg cactgtctca acgagagact 2040 cggtgaaatt atagtacctg tgaagatgca ggttacccgc gacaggacgg aaagaccccg 2100 tggagcttta ctgcaacctg atatggaatg tttgtaccgc ttgtacagga taggtaggag 2160 ccgaagagac gtgtgcgcta gcatacgagg aggcaatggt gggatactac cctggctgta 2220 tgaccattct aacccgccac gcttagcgcg tggggagaca gtgtcaggtg ggcagtttga 2280 ctggggcggt cgcctcctaa agagtaacgg aggcgcccaa aggttccctc agaatggatg 2340 gaaatcattc gcagagtgta aaggcacaag ggagcttgac tgcgagactg acaagtcgag 2400 cagggacgaa agtcgggctt agtgatccgg tggttccgca tggaagggcc atcgctcaac 2460 ggataaaagc taccccgggg ataacaggct tatctccccc aagagtccac atcgacgggg 2520 aggtttggca cctcgatgtc ggctcgtcgc atcctggggc tgtagtcggt cccaagggtt 2580 gggctgttcg cccattaaag cggcacgcga gctgggttca gaacgtcgtg agacagttcg 2640 gtccctatcc gtcgcgggcg caggaaattt gagaggagct gtccttagta cgagaggacc 2700 gggatggaca caccgctggt gtaccagttg ttccgccagg agcatcgctg ggtagctatg 2760 tgtggcaggg ataaacgctg aaagcatcta agcgtgaagc ccccctcaag atgagatttc 2820 ccatttcttc ggaaagtaag atccctgaaa gatgatcagg tagataggtt tggagtggaa 2880 gtgtagcgat acatggagcg gacaaatact aatcgatcga ggacttaacc aa 2932 54 2923 DNA Staphylococcus aureus 54 gattaagtta ttaagggcgc acggtggatg ccttggcact agaagccgat gaaggacgtt 60 actaacgacg atatgctttg gggagctgta agtaagcttt gatccagaga tttccgaatg 120 gggaaaccca gcatgagtta tgtcatgtta tcgatatgtg aatacatagc atatcagaag 180 gcacacccgg agaactgaaa catcttagta cccggaggaa gagaaagaaa attcgattcc 240 cttagtagcg gcgagcgaaa cgggaagagc ccaaaccaac aagcttgctt gttggggttg 300 taggacactc tatacggagt tacaaaggac gacattagac gaatcatctg gaaagatgaa 360 tcaaagaagg taataatcct gtagtcgaaa atgttgtctc tcttgagtgg atcctgagta 420 cgacggagca cgtgaaattc cgtcggaatc tgggaggacc atctcctaag gctaaatact 480 ctctagtgac cgatagtgaa ccagtaccgt gagggaaagg tgaaaagcac cccggaaggg 540 gagtgaaata gaacctgaaa ccgtgtgctt acaagtagtc agagcccgtt aatgggtgat 600 ggcgtgcctt ttgtagaatg aaccggcgag ttacgatttg atgcaaggtt aagcagtaaa 660 tgtggagccg tagcgaaagc gagtctgaat agggcgttta gtatttggtc gtagacccga 720 aaccaggtga tctacccttg gtcaggttga agttcaggta acactgaatg gaggaccgaa 780 ccgacttacg ttgaaaagtg agcggatgaa ctgagggtag cggagaaatt ccaatcgaac 840 ctggagatag ctggttctct ccgaaatagc tttagggcta gcctcaagtg atgattattg 900 gaggtagagc actgtttgga cgaggggccc ctctcgggtt accgaattca gacaaactcc 960 gaatgccaat taatttaact tgggagtcag aacatgggtg ataaggtccg tgttcgaaag 1020 ggaaacagcc cagaccacca gctaaggtcc caaaatatat gttaagtgga aaaggatgtg 1080 gcgttgccca gacaactagg atgttggctt agaagcagcc atcatttaaa gagtgcgtaa 1140 tagctcacta gtcgagtgac actgcgccga aaatgtaccg gggctaaaca tattaccgaa 1200 gctgtggatt gtcctttgga caatggtagg agagcgttct aagggcgttg aagcatgatc 1260 gtaaggacat gtggagcgct tagaagtgag aatgccggtg tgagtagcga aagacgggtg 1320 agaatcccgt ccaccgattg actaaggttt ccagaggaag gctcgtccgc tctgggttag 1380 tcgggtccta agctgaggcc gacaggcgta ggcgatggat aacaggttga tattcctgta 1440 ccacctataa tcgttttaat cgatgggggg acgcagtagg ataggcgaag cgtgcgattg 1500 gattgcacgt ctaagcagta aggctgagta ttaggcaaat ccggtactcg ttaaggctga 1560 gctgtgatgg ggagaagaca ttgtgtcttc gagtcgttga tttcacactg ccgagaaaag 1620 cctctagata gaaaataggt gcccgtaccg caaaccgaca caggtagtca agatgagaat 1680 tctaaggtga gcgagcgaac tctcgttaag gaactcggca aaatgacccc gtaacttcgg 1740 gagaaggggt gctctttagg gttaacgccc agaagagccg cagtgaatag gcccaagcga 1800 ctgtttatca aaaacacagg tctctgctaa accgtaaggt gatgtatagg ggctgacgcc 1860 tgcccggtgc tggaaggtta agaggagtgg ttagcttctg cgaagctacg aatcgaagcc 1920 ccagtaaacg gcggccgtaa ctataacggt cctaaggtag cgaaattcct tgtcgggtaa 1980 gttccgaccc gcacgaaagg cgtaacgatt tgggcactgt ctcaacgaga gactcggtga 2040 aatcatagta cctgtgaaga tgcaggttac ccgcgacagg acggaaagac cccgtggagc 2100 tttactgtag cctgatattg aaattcggca cagcttgtac aggataggta ggagcctttg 2160 aaacgtgagc gctagcttac gtggaggcgc tggtgggata ctaccctagc tgtgttggct 2220 ttctaacccg caccacttat cgtggtggga gacagtgtca ggcgggcagt ttgactgggg 2280 cggtcgcctc ctaaaaggta acggaggcgc tcaaaggttc cctcagaatg gttggaaatc 2340 attcatagag tgtaaaggca taagggagct tgactgcgag acctacaagt cgagcagggt 2400 cgaaagacgg acttagtgat ccggtggttc cgcatggaag ggccatcgct caacggataa 2460 aagctacccc ggggataaca ggcttatctc ccccaagagt tcacatcgac ggggaggttt 2520 ggcacctcga tgtcggctca tcgcatcctg gggctgtagt cggtcccaag ggttgggctg 2580 ttcgcccatt aaagcggtac gcgagctggg ttcagaacgt cgtgagacag ttcggtccct 2640 atccgtcgtg ggcgtaggaa atttgagagg agctgtcctt agtacgagag gaccgggatg 2700 gacatacctc tggtgtacca gttgtcgtgc caacggcata gctgggtagc tatgtgtgga 2760 cgggataagt gctgaaagca tctaagcatg aagcccccct caagatgaga tttcccaact 2820 tcggttataa gatccctcaa agatgatgag gttaataggt tcgaggtgga agcatggtga 2880 catgtggagc tgacgaatac taatcgatcg aagacttaat caa 2923 55 2900 DNA Streptococcus mutans 55 gttaagttaa taagggcgca cggtggatgc ctaggcacta ggagccgatg aaggacgtga 60 cgaacgacga catgctttgg ggagctgtaa gtaagccttg atccagagat atccgaatgg 120 gggaacccaa caggtaatgc ctgttatcca taactgttaa ggttatgaga aggaagacgc 180 agtgaactga aacatctcag tagctgcagg aagagaaagc aagagcgatt gcctcagtag 240 cggcgagcga agaggcagga gggcaaacca gagtgtttac actctggggt tgtaggactg 300 cgataaagca gccaagggaa tagaagaaga ctctgggaag agtcgccaga gagagtaaga 360 gcctcgtatt tgaaattcac ttgatgccaa gcaggatcct gagtacggcg ggacacgagg 420 aatcccgtcg gaatctggga ggcccatctc ccaaccctaa atactcccta gtgaccgata 480 gtgaaccagt accgtgaggg aaaggtgaaa agtaccccgg aaggggagtg aaagagaacc 540 tgaaaccgtg tgcttacaag aagttcgagc ccgttaatgg gtgagagcgt gccttttgta 600 gaatgaaccg gcgagttacg tttacgtgcg aggttaagtt gaagagacgg agccgtaggg 660 aaaccgagtc tgaaaagggc ggttaagtac gtagatgtag acccgaaacc aagtgaccta 720 cccatgagca ggttgaaggt gcggtaaaac gcactggagg accgaaccag gacacgttga 780 aaagtgtttg gatgacttgt gggtagcgga gaaattccaa acgaacttgg agatagctgg 840 ttctctccga aatagcttta gggctagcgt cggtcgcgag actcttggag gtagagcact 900 gtttgattga ggggtccatc ccggattacc aatctcagat aaactccgaa tgccaacgag 960 ttaagaccgg cagtcagact gcgagtgcta agatccgtag tcgaaaggga aacagcccag 1020 accaccagct aaggtcccca aataattgtt aagtggaaaa ggatgtgggg ttgcacagac 1080 aactaggatg ttagcttaga agcagctatt cattcaaaga gtgcgtaata gctcactagt 1140 cgagtgaccc tgcgccgaaa atgtaccggg gctgaaacaa tttaccgaag ctgtggatcc 1200 cttaggggat ggtaggagag cgttctatgt gcgcagaagg tgtaccgcaa ggagcgctgg 1260 agtgcataga agtgagaatg ccggtatgag tagcgtaaga caggtgagaa tcctgtccac 1320 cgtaagacta aggattccag gggaaggctc gtccgccctg ggttagtcgg gacctaagga 1380 gagaccgata ggtgtatccg atgggcaaca ggttgatatt cctgtactag agtattgagt 1440 gaaggaggga cgcagcaggc taactagagc gtgcgattgg aagagcacgt ccaagcagtg 1500 aggtgaggac tgagtcaaat gcttagttct gcgccaccaa gctgtgacgg ggagcgaagt 1560 ttagtagcga agctagtgat gtcactctgc caagaaaagc ttctagcgtt aatgaatact 1620 ctacccgtac cgcaaaccga cacaggtagt cgaggcgagt agcctcaggt gatcgagcga 1680 actctcgtta aggaactcgg caaaatggcc ccgtaacttc gggagaaggg gcgctggcga 1740 taagtcagcc gcagtgaaaa ggcccaagca actgtttatc aaaaacacag ctctctgcga 1800 aatcgtaaga tgaagtatag ggggtgacgc ctgcccggtg ctggaaggtt aagaggagcg 1860 cttagacgtt tgtcgaaggt gtgaattgaa gccccagtaa acggcggccg taactataac 1920 ggtcctaagg tagcgaaatt ccttgtcggg taagttccga cccgcacgaa aggcgtaatg 1980 atttgggcac tgtctcaacg agagactcgg tgaaatttta gtacctgtga agatgcaggt 2040 tacccgcgac aggacggaaa gaccccatgg agctttactg cagtttgata ttgcgtatct 2100 gttacacatg tacaggatag gtaggagcca aggaagagtg aacgctagtt tacttggagg 2160 cgttgttggg atactaccct tgtgtgatgg ctactctaac ccggtaggtt gatcatctac 2220 ggagacagtg tctgacgggc agtttgactg gggcggtcgc ctcctaaagc gtaacggagg 2280 cgcccaaagg ttccctcaga ctggttggaa atcagtcgta gagtgtaaag gtataaggga 2340 gcttgactgc gagacagaca agtcgagcag ggacgaaagt cgggcttagt gatccggtgg 2400 taccgtatgg aagggccatc gctcaacgga taaaagctac cctggggata acaggcttat 2460 ctcccccaag agttcacatc gacggggagg tttggcacct cgatgtcggc tcgtcgcatc 2520 ctggggctgt agtcggtccc aagggttggg ctgttcgccc attaaagcgg cacgcgagct 2580 gggttcagaa cgtcgtgaga cagttcggtc cctatccgtc gcgggcgaag gaaatttgag 2640 aggatctgct cctagtacga gaggaccaga gtggacttac cgctggtgta ccagttgttc 2700 tgccaagagc atcgctgggt agctaagtag ggaggggata aacgctgaaa gcatctaagt 2760 gtgaagcccc cctcaagatg agatttccca taacgttcag ttagtaagag ccctgaaaga 2820 agaacaggta gataggttgg gagtggaagc gttgtgagac gtgaagcgga ccaatactaa 2880 tcgctcgagg acttatccaa 2900 56 2902 DNA Streptococcus pneumoniae 56 ggttaagtta ataagggcgc acggtggatg ccttggcact aggagccgac gaaggacgtg 60 acaaacgacg atatgccttg ggtagctgta agtaagcgat gatccaggga tttccgaatg 120 ggggaaccca acaggtaata cctgttaccc acatctgtta aggatgtgag gaggaagacg 180 cagtgaactg aaacatctaa gtagctgcag gaagagaaag caaaagcgat tgccttagta 240 gcggcgagcg aaacggcaga agggcaaacc gaagagttta ctcttcgggg ttgtaggact 300 gcaatgtgga ctcaaagatt atagaagaat gatttgggaa gatcagccaa agagagtaat 360 agcctcgtat ttaaaatagt ctttgtactt agcagtatcc tgagtacggc gggacacgtg 420 aaatcccgtc ggaatctggg aggaccatct cccaacccta aatactccct agtgaccgat 480 agtgaaccag taccgtgagg gaaaggtgaa aagcaccccg ggaggggagt gaaatagaac 540 ctgaaaccgt gtgcctacaa caagttcgag cccgttaatg ggtgagagcg tgccttttgt 600 agaatgaacc ggcgagttac gttatgatgc gaggttaagt tgaagagacg gagccgtagg 660 gaaaccgagt ctgaataggg cgccttagta tcatgacgta gacccgaaac catgtgacct 720 acccatgagc aggttgaagg tgcggtaaga cgcactggag gaccgaacca gggcacgttg 780 aaaagtgctt ggatgacttg tgggtagcgg agaaattcca aacgaacttg gagatagctg 840 gttctctccg aaatagcttt agggctagcg tcgacattag agattcttgg aggtagagca 900 ctgtttgggt gaggggtcca tcccggatta ccaatctcag ataaactccg aatgccaatg 960 aattatggtc ggcagtcaga ctgcgagtgc taagatccgt agtcgaaagg gaaacagccc 1020 agaccaccag ctaaggtccc aaaataattg ttaagtggaa aaggatgtgg ggttgcacag 1080 acaactagga tgttagctta gaagcagcta ttcattcaaa gagtgcgtaa tagctcacta 1140 gtcgagtgac cctgcgccga aaatgtaccg gggctaaaac aatttaccga agctgtggat 1200 acctttatag gtatggtagg agagcgttct atgtgtgatg aaggtatacc gtgaggagtg 1260 ctggaacgca tagaagtgag aatgccggta tgagtagcga aagacaggtg agaatcctgt 1320 ccaccgtaag actaaggttt ccaggggaag gctcgtccgc cctgggttag tcgggaccta 1380 aggagagacc gaaaggtgta tccgatggac aacaggttga tattcctgta ctagagtatg 1440 tagtgatgga gggacgcagt aggctaacta aagcagacga ttggaagagt ctgtctaagc 1500 agtgaggtgt gaattgagtc aaatgcttaa ttctataaca ttgagctgtg atggggagcg 1560 aagtttagta gcgaagttag tgacgtcaca ctgccaagaa aagcttctag cgtttaaaca 1620 tactctaccc gtaccgcaaa ccgacacagg tagtcgaggc gagtagcctc aggtgagcga 1680 gagaactctc gttaaggaac tcggcaaaat gaccccgtaa cttcgggaga aggggtgctg 1740 acttaaagtc agccgcagtg aataggccca agcaactgtt tatcaaaaac acagctctct 1800 gctaaatcgt aagatgatgt atagggggtg acgcctgccc ggtgctggaa ggttaagagg 1860 agtgcttagc gtaagcgaag gtatgaattg aagccccagt aaacggcggc cgtaactata 1920 acggtcctaa ggtagcgaaa ttccttgtcg ggtaagttcc gacccgcacg aaaggcgtaa 1980 tgatttgggc actgtctcaa cgagagactc ggtgaaattt tagtacctgt gaagatgcag 2040 gttacccgcg acaggacgga aagaccccat ggagctttac tgcagtttga tattgagtgt 2100 ctgtaccaca tgtacaggat aggtaggagt ctaagagatc gggacgccag tttcgaagga 2160 gacgctgttg ggatactacc cttgtgttat ggccactcta acccagatag gtgatcccta 2220 tcggagacag tgtctgacgg gcagtttgac tggggcggtc gcctcctaaa aggtaacgga 2280 ggcgcccaaa ggttccctca gaatggttgg aaatcattcg cagagtgtaa aggtataagg 2340 gagcttgact gcgagagcta caactcgagc agggacgaaa gtcgggctta gtgatccggt 2400 ggttccgtat ggaagggcca tcgctcaacg gataaaagct accctgggga taacaggctt 2460 atctccccca agagttcaca tcgacgggga ggtttggcac ctcgatgtcg gctcgtcgca 2520 tcctggggct gtagtcggtc ccaagggttg ggctgttcgc ccattaaagc ggcacgcgag 2580 ctgggttcag aacgtcgtga gacagttcgg tccctatccg tcgcgggcgt aggaaatttg 2640 agaggatctg ctcctagtac gagaggacca gagtggactt accgctggtg taccagttgt 2700 cttgccaaag gcatcgctgg gtagctatgt agggaaggga taaacgctga aagcatctaa 2760 gtgtgaaacc cacctcaaga tgagatttcc catgattata tatcagtaag agccctgaga 2820 gatgatcagg tagataggtt agaagtggaa gtgtggcgac acatgtagcg gactaatact 2880 aatagctcga ggacttatcc aa 2902 57 2901 DNA Streptococcus pyogenes 57 ggttaagtta ataagggcgc acggtggatg ccttggcact agaagccgaa gaaggacgtg 60 actaacgacg aaatgctttg gggagctgta agtaagcgct gatccagaga tgtccgaatg 120 ggggaacccg gcatgtaatg catgtcatcc atgactgtta aggtcatgag aaggaagacg 180 cagtgaactg aaacatctaa gtagctgcag gaagagaaag caaacgcgat tgccttagta 240 gcggcgagcg aaacggcagg agggcaaacc gaggagttta ctcctcgggg ttgtaggact 300 gcgaagtggg acataaagtt aatagaagaa ttacctggga aggtaagcca aagagagtaa 360 cagcctcgta tttaaaattg actttagccc tagcagtatc ctgagtacgg cgagacacgc 420 gaaatctcgt cggaatctgg gaggaccatc tcccaaccct aaatactctc tagtgaccga 480 tagtgaacca gtaccgtgag ggaaaggtga aaagcacccc gggaggggag tgaaatagaa 540 cctgaaaccg tgtgcctaca acaagttcga gcccgttaat gggtgagagc gtgccttttg 600 tagaatgaac cggcgagtta cgatatgatg cgaggttaag ttgaagagac ggagccgtag 660 ggaaaccgag tcttaatagg gcgtcatagt atcatgttgt agacccgaaa ccatgtgacc 720 tacccatgag caggttgaag gtgtggtaaa acgcactgga ggaccgaacc agggcacgtt 780 gaaaagtgct tggatgactt gtgggtagcg gagaaattcc aaacgaactt ggagatagct 840 ggttctctcc gaaatagctt tagggctagc gtcgatgtta agtctcttgg aggtagagca 900 ctgtttgggt gaggggtcca tcccggatta ccaatctcag ataaactccg aatgccaacg 960 agatataatc ggcagtcaga ctgcgagtgc taagatccgt agtcgaaagg gaaacagccc 1020 agaccaccag ctaaggtccc aaaataactg ttaagtggaa aaggatgtgg ggttgcacag 1080 acaactagga tgttagctta gaagcagcta ttcattcaaa gagtgcgtaa tagctcacta 1140 gtcgagtgac cctgcgccga aaatgtaccg gggctaaaac agtttaccga agctgtggat 1200 gacacaaaag tgtcatggta ggagagcgtt ctatgtgtga agaaggtgta ccgtgaggag 1260 cgctggaacg catagaagtg agaatgccgg tatgagtagc gaaagacagg tgagaatcct 1320 gtccaccgta agactaaggt ttccagggga aggctcgtcc gccctgggtt agtcgggacc 1380 taaggagaga ccgaaaggtg tatccgatgg ccaacaggtt gatattcctg tactagagta 1440 tatagtgatg gagggacgca gtaggctaac taaaccggac gattggaaga gtccggctaa 1500 gcagtgaggt gtaagatgag tcaaatgctt atctttataa cattgagctg tgatggggag 1560 cgaattttag tagcgaagtt agtgatgtca cactgccaag aaaagcttct agcgtttaat 1620 gatactctac ccgtaccgca aaccgacaca ggtagtcgag gcgagtagcc tcaggtgatc 1680 gagagaactc tcgttaagga actcggcaaa atgaccccgt aacttcggga gaaggggtgc 1740 tgacttaggt cagccgcagt gaataggccc aagcaactgt ttatcaaaaa cacagctctc 1800 tgctaaatcg taagatgatg tatagggggt gacgcctgcc cggtgctgga aggttaagag 1860 gagggtttag cgcaagcgaa gatctgaatt gaagccccag taaacggcgg ccgtaactat 1920 aacggtccta aggtagcgaa attccttgtc gggtaagttc cgacccgcac gaaaggcgta 1980 atgatttggg cactgtctca acgagagact cggtgaaatt ttagtacctg tgaagatgca 2040 ggttacccgc gacaggacgg aaagacccca tggagcttta ctgcagtttg atattgagta 2100 tctgtaccac atgtacagga taggtaggag ccattgactt cgggacgcca gtttcgaatg 2160 aggcgttgtt gggatactac ccttgtgtta tggctactct aacccagata ggttatccct 2220 atcggagaca gtgtctgacg ggcagtttga ctggggcggt cgcctcctaa agagtaacgg 2280 aggcgcccaa aggttccctc agattggttg gaaatcaatc gcagagtgta aaggtataag 2340 ggagcttgac tgcgagagct acaactcgag cagggacgaa agtcgggctt agtgatccgg 2400 tggtaccgaa tggaagggcc atcgctcaac ggataaaagc taccctgggg ataacaggct 2460 tatctccccc aagagttcac atcgacgggg aggtttggca cctcgatgtc ggctcgtcgc 2520 atcctggggc tgtagtcggt cccaagggtt gggctgttcg cccattaaag cggcacgcga 2580 gctgggttca gaacgtcgtg agacagttcg gtccctatcc gtcgcgggcg taggaaattt 2640 gagaggatct gctcctagta cgagaggacc agagtggact taccgctggt gtaccagttg 2700 tcttgccaaa ggcatcgctg ggtagctatg tagggaaggg ataagcgctg aaagcatcta 2760 agtgcgaagc ccccctcaag atgagatttc ccatgatttt atatcagtaa gagccctgag 2820 agatgatcag gtagataggt taggagtgta agtgtagcga tacatgtagc ggactaatac 2880 taatagctcg aggacttatc c 2901 58 3107 DNA Mycobacterium avium 58 tgtgtgtaag taagtgttta agggcgcatg gtggatgcct tggcatcgag agccgatgaa 60 ggacgtggga ggctgcgata tgcctcgggg agctgtcaac cgagcattga tccgaggatt 120 tccgaatggg ggaacccagc acgagtgatg tcgtgttacc cgtatctgaa tatatagggt 180 gcgggaggta acgcggggaa gtgaaacatc tcagtacccg taggagaaga aaacaattgt 240 gattccgtca gtagtggcga gcgaaccgga acaggctaaa ccgcatgcat ggacaaccgg 300 gtaggggttg tgtgtgcggg gttgtgggat tgatatgtct cagctctacc tggctgaggg 360 gtagtcagaa agtgtcgtgg ttagcggaag tggcctggga cggcccgccg tagacggtga 420 gagcccggta cgcgaaaacc cggcacctgc cttatatcaa cacccgagta gcagcgggcc 480 cgtggaatct gctgtgaatc tgccgggacc acccggtaag cctaaatact tctcgatgac 540 cgatagcgga ttagtaccgt gagggaatgg tgaaaagtac cccgggaggg agtgaaatag 600 tacctgaaac cgtgtgccta caatccgtca gagcctcctc gtggggtgat ggcgtgcctt 660 ttgaagaatg agcctgcgag tcagggacac gtcgcgaggt taacccgtgc ggggtagccg 720 cagcgaaagc gagtctgaat agggcgcatc ccctttgggg tgtagtggcg tgttctggac 780 ccgaagcgga gtgatctacc catggccagg gtgaagcgcg ggtaagaccg cgtggaggcc 840 cgaacccact taggttgaag actgagggga tgagctgtgg gtaggggtga aaggccaatc 900 aaactccgtg atagctggtt ctccccgaaa tgcatttagg tgcagcgttg cgtggttcac 960 cacggaggta gagctactgg atggccgatg ggccctacta ggttactgac gtcagccaaa 1020 ctccgaatgc cgtggtgtaa aagcgtggca gtgagacggc gggggataag ctccgtacgt 1080 cgaaagggaa acagcccaga tcgccggcta aggcccctaa gcgtgtgcta agtggaaaag 1140 gatgtgtagt cgcagagaca accaggaggt tggcttagaa gcagccatcc ttgaaagagt 1200 gcgtaatagc tcactggtca agtgattatg cgccgataat gtagcggggc tcaagcacac 1260 cgccgaagcc gcggcacatt catctttacg gtggatgtgg gtaggggagc gtcccccatt 1320 cagcgaagct ccgggtgacc ggtggtggag ggtgggggag tgagaatgca ggcatgagta 1380 gcgataaggc aagtgagaac cttgcccgcc gtaagaccaa gggttcctgg gccaggccag 1440 tccgcccagg gtgagtcggg acctaaggcg aggccgacag ggtagtcgat ggacaacggg 1500 ttgatattcc cgtacccgtg tatgggcgtc cctgatgaat cagcggtact aaccacccaa 1560 aaccggatcg accattcccc ttcgggggcg tggcgattcg gggctgcgtg ggaccttcgc 1620 tggtagtagt caagcaatgg ggtgacgcag gaaggcagcc gtaccagtca gtggtaatac 1680 tggggcaagc ccgtagagag cgataggcaa atccgtcgct cactaatcct gagaggtgat 1740 gcatagccgg ttgaggcgaa ttcggtgatc ctctgctgcc aagaaaagcc tctagcgagc 1800 acatacacgg cccgtacccc aaaccaacac aggtggtcag gtagagaata ccaaggcgta 1860 cgagataact atggttaagg aactcggcaa aatgcccccg taacttcggg agaagggggc 1920 ccggaatacc gtgaacaccc ttgcggtggg agcgggattc ggccgcagaa accagtgggt 1980 agcgactgtt tactaaaaac acaggtccgt gcgaagtcgc aagacgatgt atacggactg 2040 acgcctgccc ggtgctggaa ggttaagagg acccgttaac ccgtaagggt gaagcggaga 2100 atttaagccc cagtaaacgg cggtggtaac tataaccatc ctaaggtagc gaaattcctt 2160 gtcgggtaag ttccgacctg cacgaatggc gtaacgactt cccaactgtc tcaaccatag 2220 actcggcgaa attgcactac gagtaaagat gctcgttacg cgcggcagga cgaaaagacc 2280 ccgggacctt cactacaact tggtattggt gttcggtacg gtttgtgtag gataggtggg 2340 agactttgaa gcacagacgc cagtttgtgt ggagtcgttg ttgaaatacc actctgatcg 2400 tattggacac ctaacgtcga acccttatcg ggttcacgga cagtgcctgg cgggtagttt 2460 aactggggcg gttgcctcct aaaatgtaac ggaggcgccc aaaggttccc tcaacctgga 2520 cggcaatcag gtggcgagtg taagtgcaca agggagcttg actgcgagac ttacaagtca 2580 agcagggacg aaagtcggga ctagtgatcc ggcacccccg agtggaaggg gtgtcactca 2640 acggataaaa ggtaccccgg ggataacggg ctgatcttcc ccaagagtcc atatcgacgg 2700 gatggtttgg cacctcgatg tcggctcgtc gcatcctggg gctggagcag gtcccaaagg 2760 ttgggctgtt cgcccattaa agcggcacgc gagctgggtt tagaacgtcg tgagacagtt 2820 cggtctctat ccgccgcgcg cgtcagaaac ttgaggaaac ctgtccctag tacgagagga 2880 ccgggacgga cgaacctctg gtataccagt tgtcccacca ggggcacggc tggatagcca 2940 cgttcggaca ggataaccgc tgaaagcatc taagcgggaa accttctcca agatcaggtt 3000 tctcaccctt ttagagggat aaggcccccc gcagaccacg ggattgatag gccagacctg 3060 gaagctcagt aatgagtgca gggaactggc actaactggc cgaaagc 3107 59 3138 DNA Mycobacterium tuberculosis 59 ttgtaagtgt ctaagggcgc atggtggatg ccttggcatc gagagccgat gaaggacgtg 60 ggaggctgcg atatgcctcg gggagctgtc aaccgagcgt ggatccgagg atttccgaat 120 ggggaaaccc agcacgagtg atgtcgtgct acccgcatct gaatatatag ggtgcgggag 180 ggaacgcggg gaagtgaaac atctcagtac ccgtaggagg agaaaacaat tgtgattccg 240 caagtagtgg cgagcgaacg cggaacaggc taaaccgcac gcatgggtaa ccgggtaggg 300 gttgtgtgtg cggggttgtg ggaggatatg tctcagcgct acccggctga gaggcagtca 360 gaaagtgtcg tggttagcgg aagtggcctg ggatggtctg ccgtagacgg tgagagcccg 420 gtacgcgaaa acccggcacc tgcctagtat caattcccga gtagcagcgg gcccgtggaa 480 tccgctgtga atccgccggg accacccggt aagcctaaat actcctcgat gaccgatagc 540 ggattagtac cgtgagggaa tggtgaaaag taccccggga ggggagtgaa agagtacctg 600 aaaccgtgtg cctacaatcc gtcagagcct ccttttcctc tccggaggag ggtggtgatg 660 gcgtgccttt tgaagaatga gcctgcgagt cagggacatg tcgcaaggtt aacccgtgtg 720 gggtagccgc agcgaaagcg agtctgaata gggcgaccca cacgcgcata cgcgcgtgtg 780 aatagtggcg tgttctggac ccgaagcgga gtgatctacc catggccagg gtgaagcgcg 840 ggtaagaccg cgtggaggcc cgaacccact taggttgaag actgagggga tgagctgtgg 900 gtaggggtga aaggccaatc aaactccgtg atagctggtt ctccccgaaa tgcatttagg 960 tgcagcgttg cgtggttcac cgcggaggta gagctactgg atggccgatg ggccctacta 1020 ggttactgac gtcagccaaa ctccgaatgc cgtggtgtaa agcgtggcag tgagacggcg 1080 ggggataagc tccgtacgtc gaaagggaaa cagcccagat cgccggctaa ggcccccaag 1140 cgtgtgctaa gtgggaaagg atgtgcagtc gcaaagacaa ccaggaggtt ggcttagaag 1200 cagccaccct tgaaagagtg cgtaatagct cactggtcaa gtgattgtgc gccgataatg 1260 tagcggggct caagcacacc gccgaagccg cggcacatcc accttgtggt gggtgtgggt 1320 aggggagcgt ccctcattca gcgaagccac cgggtgaccg gtggtggagg gtgggggagt 1380 gagaatgcag gcatgagtag cgacaaggca agtgagaacc ttgcccgccg aaagaccaag 1440 ggttcctggg ccaggccagt ccgcccaggg tgagtcggga cctaaggcga ggccgacagg 1500 cgtagtcgat ggacaacggg ttgatattcc cgtacccgtg tgtgggcgcc cgtgacgaat 1560 cagcggtact aaccacccaa aaccggatcg atcactcccc ttcgggggtg tggagttctg 1620 gggctgcgtg ggaacttcgc tggtagtagt caagcgaagg ggtgacgcag gaaggtagcc 1680 gtaccagtca gtggtaacac tggggcaagc cggtagggag agcgataggc aaatccgtcg 1740 ctcactaatc ctgagaggtg acgcatagcc ggttgaggcg aattcggtga tcctctgctg 1800 ccaagaaaag cctctagcga gcacacacac ggcccgtacc ccaaaccgac acaggtggtc 1860 aggtagagca taccaaggcg tacgagataa ctatggttaa ggaactcggc aaaatgcccc 1920 cgtaacttcg ggagaagggg gaccggaata tcgtgaacac ccttgcggtg ggagcgggat 1980 ccggtcgcag aaaccagtga ggagcgactg tttactaaaa acacaggtcc gtgcgaagtc 2040 gcaagacgat gtatacggac tgacgcctgc ccggtgctgg aaggttaaga ggacccgtta 2100 acccgcaagg gtgaagcgga gaatttaagc cccagtaaac ggcggtggta actataacca 2160 tcctaaggta gcgaaattcc ttgtcgggta agttccgacc tgcacgaatg gcgtaacgac 2220 ttctcaactg tctcaaccat agactcggcg aaattgcact acgagtaaag atgctcgtta 2280 cgcgcggcag gacgaaaaga ccccgggacc ttcactacaa cttggtattg atgttcggta 2340 cggtttgtgt aggataggtg ggagactgtg aaacctcgac gccagttggg gcggagtcgt 2400 tgttgaaata ccactctgat cgtattgggc atctaacctc gaaccctgaa tcgggtttag 2460 ggacagtgcc tggcgggtag tttaactggg gcggttgcct cctaaaatgt aacggaggcg 2520 cccaaaggtt ccctcaacct ggacggcaat caggtggcga gtgtaaatgc acaagggagc 2580 ttgactgcga gacttacaag tcaagcaggg acgaaagtcg ggattagtga tccggcaccc 2640 ccgagtggaa ggggtgtcgc tcaacggata aaaggtaccc cggggataac aggctgatct 2700 tccccaagag tccatatcga cgggatggtt tggcacctcg atgtcggctc gtcgcatcct 2760 ggggctggag caggtcccaa gggttgggct gttcgcccat taaagcggca cgcgagctgg 2820 gtttagaacg tcgtgagaca gttcggtctc tatccgccgc gcgcgtcaga aacttgagga 2880 aacctgtccc tagtacgaga ggaccgggac ggacgaacct ctggtgcacc agttgtcccg 2940 ccaggggcac cgctggatag ccacgttcgg tcaggataac cgctgaaagc atctaagcgg 3000 gaaaccttct ccaagatcag gtttctcacc cacttggtgg gataaggccc cccgcagaac 3060 acgggttcaa taggtcagac ctggaagctc agtaatgggt gtagggaact ggtgctaacc 3120 ggccgaaaac ttacaaca 3138 60 2903 DNA Escherichia coli 60 ggttaagcga ctaagcgtac acggtggatg ccctggcagt cagaggcgat gaaggacgtg 60 ctaatctgcg ataagcgtcg gtaaggtgat atgaaccgtt ataaccggcg atttccgaat 120 ggggaaaccc agtgtgattc gtcacactat cattaactga atccataggt taatgaggcg 180 aaccggggga actgaaacat ctaagtaccc cgaggaaaag aaatcaaccg agattccccc 240 agtagcggcg agcgaacggg gaggagccca gagcctgaat cagtgtgtgt gttagtggaa 300 gcgtctggaa aggcgcgcga tacagggtga cagccccgta cacaaaaatg cacatactgt 360 gagctcgatg agtagggcgg gacacgtggt atcctgtctg aatatggggg gaccatcctc 420 caaggctaaa tactcctgac tgaccgatag tgaaccagta ccgtgaggga aaggcgaaaa 480 gaaccccggc gaggggagtg aaaaagaacc tgaaaccgtg tacgtacaag cagtgggagc 540 ctcttttatg gggtgactgc gtaccttttg tataatgggt cagcgactta tattctgtag 600 caaggttaac cgaatagggg agccgaaggg aaaccgagtc ttaaccgggc gttaagttgc 660 agggtataga cccgaaaccc ggtgatctag ccatgggcag gttgaaggtt gggtaacact 720 aactggagga ccgaaccgac taatgttgaa aaattagcgg atgacttgtg gctgggggtg 780 aaaggccaat caaaccggga gatagctggt tctccccgaa agctatttag gtagcgcctc 840 gtgaattcat ctccgggggt agagcactgt ttcggcaagg gggtcatccc gacttaccaa 900 cccgatgcaa actgcgaata ccggagaatg ttatcacggg agacatacgg cgggtgctaa 960 cgtccgtcgt gaagagggaa acaacccaga ccgccagcta aggtcccaaa gtcatggtta 1020 agtgggaaac gatgtgggaa ggcccagaca gccaggatgt tggcttagaa gcagccatca 1080 tttaaagaaa gcgtaatagc tcactggtcg agtcggcctg cgcggaagat gtaacggggc 1140 taaaccatgc accgaagctg cggcagcgac actgtgtgtt gttgggtagg ggagcgttct 1200 gtaagcctgt gaaggtgtac tgtgaggtat gctggaggta tcagaagtgc gaatgctgac 1260 ataagtaacg ataaagcggg tgaaaagccc gctcgccgga agaccaaggg ttcctgtcca 1320 acgttaatcg gggcagggtg agtcgacccc taaggcgagg ccgaaaggcg tagtcgatgg 1380 gaaacaggtt aatattcctg tacttggtgt tactgcgaag gggggacgga gaaggctatg 1440 ttggccgggc gacggttgtc ccggtttaag cgtgtaggct ggttttccag gcaaatccgg 1500 aaaatcaagg ctgaggcgtg atgacgaggc actacggtgc tgaagcaaca aatgccctgc 1560 ttccaggaaa agcctctaag catcaggtaa catcaaatcg taccccaaac cgacacaggt 1620 ggtcaggtag agaataccaa ggcgcttgag agaactcggg tgaaggaact aggcaaaatg 1680 gtgccgtaac ttcgggagaa ggcacgctga tatgtaggtg aagtccctcg cggatggagc 1740 tgaaatcagt cgaagatacc agctggctgc aactgtttat taaaaacaca gcactgtgca 1800 aacacgaaag tggacgtata cggtgtgacg cctgcccggt gccggaaggt taattgatgg 1860 ggtcagcgca agcgaagctc ttgatcgaag ccccggtaaa cggcggccgt aactataacg 1920 gtcctaaggt agcgaaattc cttgtcgggt aagttccgac ctgcacgaat ggcgtaatga 1980 tggccaggct gtctccaccc gagactcagt gaaattgaac tcgctgtgaa gatgcagtgt 2040 acccgcggca agacggaaag accccgtgaa cctttactat agcttgacac tgaacattga 2100 gccttgatgt gtaggatagg tgggaggctt tgaagtgtgg acgccagtct gcatggagcc 2160 gaccttgaaa taccaccctt taatgtttga tgttctaacg tggacccgtg atccgggttg 2220 cggacagtgt ctggtgggta gtttgactgg ggcggtctcc tcctaaagag taacggagga 2280 gcacgaaggt tggctaatcc tggtcggaca tcaggaggtt agtgcaatgg cataagccag 2340 cttgactgcg agcgtgacgg cgcgagcagg tgcgaaagca ggtcatagtg atccggtggt 2400 tctgaatgga agggccatcg ctcaacggat aaaaggtact ccggggataa caggctgata 2460 ccgcccaaga gttcatatcg acggcggtgt ttggcacctc gatgtcggct catcacatcc 2520 tggggctgaa gtaggtccca agggtatggc tgttcgccat ttaaagtggt acgcgagctg 2580 ggtttagaac gtcgtgagac agttcggtcc ctatctgccg tgggcgctgg agaactgagg 2640 ggggctgctc ctagtacgag aggaccggag tggacgcatc actggtgttc gggttgtcat 2700 gccaatggca ctgcccggta gctaaatgcg gaagagataa gtgctgaaag catctaagca 2760 cgaaacttgc cccgagatga gttctccctg accctttaag ggtcctgaag gaacgttgaa 2820 gacgacgacg ttgataggcc gggtgtgtaa gcgcagcgat gcgttgagct aaccggtact 2880 aatgaaccgt gaggcttaac ctt 2903 61 2903 DNA Klebsiella pneumoniae 61 ggttaagcga ctaagcgtac acggtggatg ccctggcagt cagaggcgat gaaggacgtg 60 ctaatctgcg aaaagcgtcg gtaaggtgat atgaaccgtt ataaccggcg atgtccgaat 120 ggggaaaccc agtgcaattc gttgcactat cgttaactga atacataggt taacgaggcg 180 aaccggggga actgaaacat ctaagtaccc cgaggaaaag aaatcaaccg agattccccc 240 agtagcggcg agcgaacggg gagcagccca gagtctgaat cagcttgtgt gttagtggaa 300 cggtctggaa agtccgacgg tacagggtga tagtcccgta caccaaaatg cacaggctgt 360 gaactcgaag agtagggcgg gacacgtggt atcctgtctg aatatggggg gaccatcctc 420 caaggctaaa tactcctgac tgaccgatag tgaaccagta ccgtgaggga aaggcgaaaa 480 gaaccccggc gaggggagtg aaaaagaacc tgaaaccgtg tacgtacaag cagtgggagc 540 accttcgggt gtgactgcgt accttttgta taatgggtca gcgacttata ttctgtagca 600 aggttaaccg tataggggag ccgcagggaa accgagtctt aactgggcgt taagttgcag 660 ggtatagacc cgaaacccgg tgatctagcc atgggcaggt tgaaggttgg gtaacactaa 720 ctggaggacc gaaccgacta atgttgaaaa attagcggat gacttgtggc tgggggtgaa 780 aggccaatca aaccgggaga tagctggttc tccccgaaag ctatttaggt agcgcctcgt 840 gaactcatct tcgggggtag agcactgttt cggctagggg gtcatcccga cttaccaacc 900 cgatgcaaac tacgaatacc gaagaatgtt atcacgggag acacacggcg ggtgctaacg 960 tccgtcgtga agagggaaac aacccagacc gccagctaag gtcccaaagt catggttaag 1020 tgggaaacga tgtgggaagg cacagacagc caggatgttg gcttagaagc agccatcatt 1080 taaagaaagc gtaatagctc actggtcgag tcggcctgcg cggaagatgt aacggggcta 1140 aaccatgcac cgaagctgcg gcagcgacac tatgtgttgt tgggtagggg agcgttctgt 1200 aagcctgcga aggtgtgctg tgaggcatgc tggaggtatc agaagtgcga atgctgacat 1260 aagtaacgat aaagcgggtg aaaagcccgc tcgccggaag accaagggtt cctgtccaac 1320 gttaatcggg gcagggtgag tcgaccccta aggcgaggcc gaaaggcgta gtcgatggga 1380 aacaggttaa tattcctgta cttggtgtta ctgcgaaggg gggacggaga aggctatgtt 1440 agccgggcga cggttgtccc ggtttaagca tgtaggctgg ttgtccaggc aaatccggat 1500 aatcaaggct gaggtgtgat gacgaggcac tacggtgctg aagtaacaaa tgctctgctt 1560 ccaggaaaag cctctaagca tcaggtaaca tcaaatcgta ccccaaaccg acacaggtgg 1620 tcaggtagag aataccaagg cgcttgagat aactcgggtg aaggaactag gcaaaatggt 1680 gccgtaactt cgggagaagg cacgctggtg tgtaggtgaa gcccctgccg ggtggagctg 1740 agaccagtcg aagataccag ctggctgcaa ctgtttatta aaaacacagc actgtgcaaa 1800 cacgaaagtg gacgtatacg gtgtgacgcc tgcccggtgc cggaaggtta attgatgggg 1860 ttatccgtaa ggagaagctc ttgatcgaag ccccggtaaa cggcggccgt aactataacg 1920 gtcctaaggt agcgaaattc cttgtcgggt aagttccgac ctgcacgaat ggcgtaatga 1980 tggccaggct gtctccaccc gagactcagt gaaattgaac tcgctgtgaa gatgcagtgt 2040 acccgcggca agacggaaag accccgtgaa cctttactat agcttgacac tgaacattga 2100 gccttgatgt gtaggatagg tgggaggctt tgaagcgtgg acgccagtct gcgtggagcc 2160 aaccttgaaa taccaccctt taatgtttga tgttctaacg ttggcccctc accggggttg 2220 cggacagtgt ctggtgggta gtttgactgg ggcggtctcc tcccaaagcg taacggagga 2280 gcacgaaggt tagctaatcc tggtcggaca tcaggaggtt agtgcaatgg cataagctag 2340 cttgactgcg agcgtgacgg cgcgagcagg tgcgaaagca ggtcatagtg atccggtggt 2400 tctgaatgga agggccatcg ctcaacggat aaaaggtact ccggggataa caggctgata 2460 ccgcccaaga gttcatatcg acggcggtgt ttggcacctc gatgtcggct catcacatcc 2520 tggggctgaa gtaggtccca agggtatggc tgttcgccat ttaaagtggt acgcgagctg 2580 ggtttagaac gtcgtgagac agttcggtcc ctatctgccg tgggcgctgg agaattgagg 2640 ggggctgctc ctagtacgag aggaccggag tggacgcatc actggtgttc gggttgtcat 2700 gccaatggca ctgcccggta gctaaatgcg gaagagataa gtgctgaaag catctaagca 2760 cgaaacttgc cccgagatga gttctccctg agactttaag tctcctgaag gaacgttgaa 2820 gacgacgacg ttgataggcc gggtgtgtaa gcgcagcgat gcgttgagct aaccggtact 2880 aatgaaccgt gaggcttaac ctt 2903 62 2897 DNA Haemophilus influenzae 62 gtatagttaa gtgactaagc gtacaaggtg gatgccttgg caatcagagg cgaagaagga 60 cgtgctaatc tgcgaaaagc ttggatgagt cgataagagg cgtttaatcc aagatatccg 120 aatggggaaa cccagtagat gaagaatcta ctatcaacaa gtgaattcat agcttgttga 180 ggcaaaccgg gagaactgaa acatctaagt accccgagga aaagaaatca accgagattt 240 cgtcagtagc ggcgagcgaa agcgaaagag ccagtaagtg atagcaatat agtgaggaga 300 atgtgttggg aagcacaatc aaagagggtg ataatcccgt atctaaaaac catattgtgg 360 tactaagcta acgagaagta gggcgggaca cgtgatatcc tgtttgaaga aggggggccc 420 atcctccaag gctaaatact cctgattgac cgatagtgaa ccagtactgt gaaggaaagg 480 cgaaaagaac cccggtgagg ggagtgaaat agaacctgaa accttgtacg tacaagcagt 540 gggagcgagg gcaaccttgt gactgcgtac cttttgtata atgggtcagc gacttatatt 600 ttgtagcgag gttaaccgaa taggggagcc gaagggaaac cgagtcttaa ctgggcgaat 660 agttgcaagg tatagacccg aaacccggtg atctagccat gggcaggttg aaggttgggt 720 aacactaact ggaggaccga accgactaat gttgaaaaat tagcggatga cttgtggctg 780 ggggtgaaag gccaatcaaa ccgggagata gctggttctc cccgaaatct atttaggtag 840 agccttgagg tgacaccttt gggggtagag cactgtttcg gctagggggc catcccggct 900 taccaacccg atgcaaacta cgaataccaa agagtgatac tcaggagaca cacggcgggt 960 gctaacgtcc gtcgtggaga gggaaacaac ccagaccgcc agctaaggtc cccaagtcta 1020 tattaagtgg gaaacgaagt gggaaggctt agacagctag gatgttggct tagaagcagc 1080 catcatttaa agaaagcgta atagctcact agtcgagtcg gcctgcgcgg aagatgtaac 1140 ggggctgaaa tatagcaccg aagctgcggc atcagaattt attctgttgg gtaggggagc 1200 gttgtgtaag cggaagaagg ttcatcgaga ggtgggctgg acgtatcaca agtgcgaatg 1260 ctgacataag taacgataaa acgggtgaaa aacccgttcg ccggaagacc aagggttcct 1320 gtccaacgtt aatcggggca gggtgagtcg gctcctaagg cgaggctgaa aagcgtagtc 1380 gatgggaaac aggttaatat tcctgtactt ggtaaagctg cgatgtgggg acggagtagg 1440 ttaggttatc gcactgttgg atatgtgcgt ttaagttggt aggtgggaag tttaggcaaa 1500 tccggacttc cttaacacag agagatgatg acgaggctct acggagctga agtaactgat 1560 accacacttc caggaaaagc cactaagcga aaggctttac taaaccgtac tgaaaaccga 1620 cacaggtggt caggtagaga atactcaggc gcttgagaga actcgggtga aggaactagg 1680 caaaatagca ccgtaacttc gggagaaggt gcgccggcgt agattgtaag ggctagcccc 1740 tgaaggttga accggtcgaa gataccagct ggctgcaact gtttattaaa aacacagcac 1800 tctgcaaaca cgaaagtgga cgtatagggt gtgatgcctg cccggtgctg gaaggttaat 1860 tgatggtgtc atcgaaagag aagcacctga tcgaagcccc agtaaacggc ggccgtaact 1920 ataacggtcc taaggtagcg aaattccttg tcgggtaagt tccgacctgc acgaatggca 1980 taatgatggc caggctgtct ccacccgaga ctcagtgaaa ttgaaatcgc cgtgaagatg 2040 cggtgtaccc gcggctagac ggaaagaccc cgtgaacctt tactatagct tgacactgaa 2100 cattgaattt tgatgtgtag gataggtggg agcctttgaa gcagtgacgc cagtcattgt 2160 ggaggcgacc ttgaaatacc accctttaac gtttgatgtt ctaacgaaga tgacgaaacg 2220 tggtctcgga cagtgtctgg tgggtagttt gactggggcg gtctcctccc aaagcgtaac 2280 ggaggagcac gaaggtttgc taatcacggt cggacatcgt gaggttagtg caatggtata 2340 agcaagctta actgcgagac agacaagtcg agcaggtacg aaagtaggtc atagtgatcc 2400 ggtggttctg aatggaaggg ccatcgctca acggataaaa ggtactccgg ggataacagg 2460 ctgataccgc ccaagagttc atatcgacgg cggtgtttgg cacctcgatg tcggctcatc 2520 acatcctggg gctgaagtag gtcccaaggg tatggctgtt cgccatttaa agtggtacgc 2580 gagctgggtt tagaacgtcg tgagacagtt cggtccctat ctgccgtggg cgtaggatga 2640 ttgattgggg ctgctcctag tacgagagga ccggagtgga cgcatcactg gtgttccggt 2700 tgtgtcgcca gacgcattgc cgggtagcta aatgcggaag agataagtgc tgaaagcatc 2760 taagcacgaa acttgccaag agatgagtca tccctgactt taagtcagta agggttgttg 2820 tagactacga cgtagatagg ttgggtgtgt aagtgatgtg agtcattgag ctaaccaata 2880 ctaattgccc gagaggc 2897 63 2865 DNA Bordetella bronchiseptica modified_base (622) N = A, C, G or T/U 63 gatcaagcga ctaagtgcat atggtggatg ccttggcgat cacaggcgga tgaaggacgt 60 agtagcctgc gaaaagctgc ggggagctgg caaacaagca ttgatccgca gatatccgaa 120 tggggaaacc cacggcaagc ggtatccctg gctgaataca taggccagtg gaggcgaacc 180 gggtgaactg aaacatctca gtagctcgag gaaaagaaat caaccgagat tccgaaagta 240 gtggcgagcg aaatcggaag agcctttacg atttagcatt ttgcatagtc gaacggaatg 300 gaaagtccgg ccgtagcagg tgatagccct gtagacgaat gcagagtgtg gaactaggcg 360 taagagaagt agggcgggac acgtgaaatc ctgtctgaag atggggggac catcctccaa 420 ggctaaatac tcgtgatcga ccgatagtga accagtaccg tgaggaaagg cgaaaagaac 480 cccggaagga gtgaaataga tcctgaaacc gtatgcatac aacagtcgga gcctctttat 540 ggggtgacgg cgtacctttt gtataatggg tcagcgactt acattcagtg gcagcttaac 600 cgaataggga aggcgtcaga anagcagtcc gaatagggcg ttccagtcgc tgggtgtaga 660 cccgaaacca gatgatctac ccatggccag gttgaaggca cggtaacacg tgctggagga 720 ccgaacccac tagtgttgaa aaactagggg atgagctgtg gataggggtg aaaggctaaa 780 caaatctgga aatagctggt tctctccgaa aactatttag gtagtgcctc aagtattact 840 gcagggggta gagcactgtt atggctaggg ggtcatggcg acttaccaaa ccatggcaaa 900 ctccgaatac ctgcaagtac agcttgggag acagacgacc gggtgctaac gtccggactc 960 aagagggaaa caacccagac cgccagctaa ggtcccgaat tatcgctaag tgggaaacga 1020 agtgggaagg catagacagt caggaggttg gcttagaagc agccaccctt taaagaaagc 1080 gtaatagctc actgatcgag tcgtcctgcg cggaagatgt aacggctaag cgataaaccg 1140 aagctgcggg tgtgcacttt tagtgcagcg gtaggagagc gttctgtaag cctgcgaagg 1200 tggcttgtaa aggctgctgg aggtatcaga agtgcgaatg ctgacatgag tagccataaa 1260 gggggtgaaa agccccctcg ccgtaagtcc aaggtttcct gcgcaacgtt catcggcgca 1320 gggtgagtcg gcccctaagg cgaggcagag atgcgtagct gatgggaagc tggttaatat 1380 tccagcaccg tcgtacagtg cgatgggggg acggatcgcg gaaggtcatc agggtgttgg 1440 acgtccctgt tgctgcattg aagatggcgc ttaggcaaat ccgggcgcga gaatcaaggg 1500 tgtggcacga gcgagcaagt ctcgcgaagt gattggaagt ggttccaaga aaagcctcta 1560 agcttcagct gtacgagacc gtaccgcaaa ccgacacagg tgggacggga tgaatattcc 1620 aaggcgcttg agagaactca ggagaaggaa ctcggcaaat tgataccgta acttcgggag 1680 aaggtatacc ctggtagtgt gaagcctgcg cgctgagcat gaaggggtcg cagagaatcg 1740 gtggctgcga ctgtttatta aaaacacagc actctgcaaa gacgaaagtc gacgtatagg 1800 gtgtgacgcc tgcccggtgc cggaaggtta agtgatgggg tgcaagctct tgatcgaagc 1860 cccggtaaac ggcggccgta actataacgg tcctaaggta gcgaaattcc ttgtcgggta 1920 agttccgacc tgcacgaatg gcgtaacgat ggccacactg tctcctcctg agactcagcg 1980 aagttgaagt gtttgtgatg atgcaatcta cccgcggcta gacggaaaga ccccatgaac 2040 ctttactgta gctttgcatt ggactgtgaa ccggcctgtg taggataggt gggaggcgca 2100 gaactcgagt cgccagattc gagggagcca tccttgaaat accaccctgg tttgtttgcg 2160 gttctaacct tggtccgtta tccggatcgg ggacagtgca tggtaggcag tttgactggg 2220 gcggtctcct cccaaagcgt aacggaggag ttcgaaggta cgctaggtac ggtcggaaat 2280 cgtgctgata gtgcaatggc ataagcgtgc ttgactgtga gactgacagt gaacaggtgc 2340 gaacgggaca tagtgatccg gtggttctga tggaagggcc atcgctcaac ggataaaggt 2400 actctgggat aacaggctga taccgcccaa gagttcatat cgacggcggt gtttggcacc 2460 tcgatgtcgg ctcatctcat cctggggctg tagccggtcc aagggtatgc tgttcgccat 2520 ttaaagaggt acgtgagctg ggtttagaaa cgtcgtgaga cagtttggtc cctatctgcc 2580 gtgggcgttg gatacttgaa caggagcctg ctcctagtac gagaggaccg gagtggacgt 2640 acctctggtg taccggttgt catgccaatg gcattgccgg gtagctaagt acggaagaga 2700 taaccgctga aggcatctaa gcgggaaact cgtctgaaga ttaggtatcc cggggactag 2760 atccccctga agggtcgttc gagaccagga cgttgatagg tcgggtgtgg aagcgcagta 2820 atgcgttaag ctaaccgata ctaattgccc gtgaggctta atcct 2865 64 2865 DNA Bordetella parapertussis modified_base (624) N = A, C, G or T/U 64 gatcaagcga ctaagtgcat atggtggatg ccttggcgat cacaggcgat gaaggacgta 60 gtagcctgcg aaaagctgcg gggagctggc aaacaagcat tgatccgcag atatccgaat 120 ggggaaaccc acggcaagcg gtatccctgg ctgaatacat aggccagtgg aggcgaaccg 180 ggtgaactga aacatctcag tagctcgagg aaaagaaatc aaccgagatt ccgaaagtag 240 tggcgagcga aatcggaaga gcctttacga tttagcattt tgcatagtcg aacggaatgg 300 aaagtccggc cgtagcaggt gatagccctg tagacgaaat gcagagtgtg gaactaggcg 360 taagagaagt agggcgggac acgtgaaatc ctgtctgaag atggggggac catcctccaa 420 ggctaaatac tcgtgatcga ccgatagtga accagtaccg tgaggaaagg cgaaaagaac 480 cccggaagga gtgaaataga tcctgaaacc gtatgcatac aaacagtcgg agcctcttta 540 tggggtgacg gcgtaccttt tgtataatgg gtcagcgact tacattcagt ggcgagctta 600 accgaatagg gaaggcgtca gaanagcagt ccgaataggg cgtccagtcg ctgggtgtag 660 acccgaaacc agatgatcta cccatggcca ggttgaaggc acggtaacac gtcgtggagg 720 accgaaccca ctagtgttga aaaactaggg gatgagctgt ggataggggt gaaaggctaa 780 acaaatctgg aaatagctgg ttctctccga aaactattta ggtagtgcct caagtattac 840 tgcagggggt agagcactgt tatggctagg gggtcatggc gacttaccaa accatggcaa 900 actccgaata cctgcaagta cagcttggga gacagacgac cgggtgctaa cgtccggact 960 caagagggaa acaacccaga ccgccagcta aggtcccgaa ttatcgctaa gtgggaaacg 1020 aagtgggaag gcatagacag tcaggaggtt ggcttagaag cagccaccct ttaaagaaag 1080 cgtaatagct cactgatcga gtcgtcctgc gcggaagatg taacggctaa gcgataaacc 1140 gaagctgcgg gtgtgcactt ttagtgcagc ggtaggagag cgttctgtaa gcctgcgaag 1200 gtggcttgta aaggctgctg gaggtatcag aagtgcgaat gctgacatga gtagcgataa 1260 agggggtgaa aagccccctc gccgtaagtc caaggtttcc tgcgcaacgt tcatcggcgc 1320 agggtgagtc ggcccctaag gcgaggcaga gatgcgtagc tgatgggaag ctggttaata 1380 ttccagcacc gtcgtacagt gcgatggggg gacggatcgc ggaaggtcat cagggtgttg 1440 gacgtccctg ttgctgcatt gaagatggcg cttaggcaaa tccgggcgcg agaatcaagg 1500 gtgtggcacg agcgagcaag tctcgcgaag tgattggaag tggttccaag aaaagcctct 1560 aagcttcagc tgtacgagac cgtaccgcaa accgacacag gtgggacggg atgaatattc 1620 caaggcgctt gagagaactc aggagaagga actcggcaaa ttgataccgt aacttcggga 1680 gaaggtatac cctggtagtg tgaagcctgc gcgctgagca tgaaggggtc gcagagaatc 1740 ggtggctgcg actgtttatt aaaaacacag cactctgcaa agacgaaagt cgacgtatag 1800 ggtgtgacgc ctgcccggtg ccggaaggtt aagtgatggg gtgcaagctc ttgatcgaag 1860 ccccggtaaa cggcggccgt aactataacg gtcctaaggt agcgaaattc cttgtcgggt 1920 aagttccgac ctgcacgaat ggcgtaacga tggccacact gtctcctcct gagactcagc 1980 gaagttgaag tgtttgtgat gatgcaatct acccgcggct agacggaaag accccatgaa 2040 cctttactgt agctttgcat tggactgtga accggcctgt gtaggatagg tgggaggcgc 2100 agaactcgag tcgccagatt cgagggagcc atccttgaaa taccaccctg gtttgtttgc 2160 ggttctaacc ttggtccgtt atccggatcg gggacagtgc atggtaggca gtttgactgg 2220 ggcggtctcc tcccaaagcg taacggagga gttcgaaggt acgctaggta cggtcggaaa 2280 tcgtgctgat agtgcaatgg cataagcgtg cttgactgtg agactgacag tcgaacaggt 2340 gcgaacggga catagtgatc cggtggttct gatggaaggg ccatcgctca acggataaag 2400 gtactctggg ataacaggct gataccgccc aagagttcat atcgacggcg gtgtttggca 2460 cctcgatgtc ggctcatctc atcctggggc tgtagccggt ccaagggtat gctgttcgcc 2520 atttaaagag gtacgtgagc tgggtttaga aacgtcgtga gacagtttgg tccctatctg 2580 ccgtgggcgt tggatacttg aacaggagcc tgctcctagt acgagaggac cggagtggac 2640 gtacctctgg tgtaccggtt gtcatgccaa tggcattgcc gggtagctaa gtacggaaga 2700 gataaccgct gaaggcatct aagcggaaac tcgtctgaag attaggtatc ccgggactag 2760 atccccctga agggtcgttc gagaccagga cgttgatagg tcgggtgtgg aagcgcagta 2820 atgcgttaag ctaaccgata ctaattgccc gtgaggcttg atcct 2865 65 2864 DNA Bordetella pertussis modified_base (624) N = A, C, G or T/U 65 gatcaagcga ctaagtgcat atggtggatg ccttggcgat cacaggcgat gaaggacgta 60 gtagcctgcg aaaagctgcg gggagctggc aaacaagcat tgatccgcag atatccgaat 120 ggggaaaccc acggcaagcg gtatccctgg ctgaatacat aggccagtgg aggcgaaccg 180 ggtgaactga aacatctcag tagctcgagg aaaagaaatc aaccgagatt ccgaaagtag 240 tggcgagcga aatcggaaga gcctttacga tttagcattt tgcatagtcg aacggaatgg 300 aaagtccggc cgtagcaggt gatagccctg tagacgaaat gcagagtgtg gaactaggcg 360 taagagaagt agggcgggac acgtgaaatc ctgtctgaag atggggggac catcctccaa 420 ggctaaatac tcgtgatcga ccgatagtga accagtaccg tgaggaaagg cgaaaagaac 480 cccggaagga gtgaaataga tcctgaaacc gtatgcatac aaacagtcgg agcctcttta 540 tggggtgacg gcgtaccttt tgtataatgg gtcagcgact tacattcagt ggcgagctta 600 accgaatagg gaaggcgtca gaanagcagt ccgaataggg cgtccagtcg ctgggtgtag 660 acccgaaacc agatgatcta cccatggcca ggttgaaggc acggtaacac gtcgtggagg 720 accgaaccca ctagtgttga aaaactaggg gatgagctgt ggataggggt gaaaggctaa 780 acaaatctgg aaatagctgg ttctctccga aaactattta ggtagtgcct caagtattac 840 tgcagggggt agagcactgt tatggctagg gggtcatggc gacttaccaa accatggcaa 900 actccgaata cctgcaagta cagcttggga gacagacgac cgggtgctaa cgtccggact 960 caagagggaa acaacccaga ccgccagcta aggtcccgaa ttatcgctaa gtgggaaacg 1020 aagtgggaag gcatagacag tcaggaggtt ggcttagaag cagccaccct ttaaagaaag 1080 cgtaatagct cactgatcga gtcgtcctgc gcggaagatg taacggctaa gcgataaacc 1140 gaagctgcgg gtgtgcactt ttagtgcagc ggtaggagag cgttctgtaa gcctgcgaag 1200 gtggcttgta aaggctgctg gaggtatcag aagtgcgaat gctgacatga gtagcgataa 1260 agggggtgaa aagccccctc gccgtaagtc caaggtttcc tgcgcaacgt tcatcggcgc 1320 agggtgagtc ggcccctaag gcgaggcaga gatgcgtagc tgatgggaag ctggttaata 1380 ttccagcacc gtcgtacagt gcgatggggg gacggatcgc ggaaggtcat cagggtgttg 1440 gacgtccctg ttgctgcatt gaagatggcg cttaggcaaa tccgggcgcg agaatcaagg 1500 gtgtggcacg agcgagcaag tctcgcgaag tgattggaag tggttccaag aaaagcctct 1560 aagcttcagc tgtacgagac cgtaccgcaa accgacacag gtgggacggg atgaatattc 1620 caaggcgctt gagagaactc aggagaagga actcggcaaa ttgataccgt aacttcggga 1680 gaaggtatac cctggtagtg tgaagcctgc gcgctgagca tgaaggggtc gcagagaatc 1740 ggtggctgcg actgtttatt aaaaacacag cactctgcaa agacgaaagt cgacgtatag 1800 ggtgtgacgc ctgcccggtg ccggaaggtt aagtgatggg gtgcaagctc ttgatcgaag 1860 ccccggtaaa cggcggccgt aactataacg gtcctaaggt agcgaaattc cttgtcgggt 1920 aagttccgac ctgcacgaat ggcgtaacga tggccacact gtctcctcct gagactcagc 1980 gaagttgaag tgtttgtgat gatgcaatct acccgcggct agacggaaag accccatgaa 2040 cctttactgt agctttgcat tggactgtga accggcctgt gtaggatagg tgggaggcgc 2100 agaactcgag tcgccagatt cgagggagcc atccttgaaa taccaccctg gtttgtttgc 2160 ggttctaacc ttggtccgtt atccggatcg gggacagtgc atggtaggca gtttgactgg 2220 ggcggtctcc tcccaaagcg taacggagga gttcgaaggt acgctaggta cggtcggaaa 2280 tcgtgctgat agtgcaatgg cataagcgtg cttgactgtg agactgacag tcgaacaggt 2340 gcgaacggga catagtgatc cggtggttct gatggaaggg ccatcgctca acggataaag 2400 gtactctggg ataacaggct gataccgccc aagagttcat atcgacggcg gtgtttggca 2460 cctcgatgtc ggctcatctc atcctggggc tgtagccggt ccaagggtat gctgttcgcc 2520 atttaaagag gtacgtgagc tgggtttaaa acgtcgtgag acagtttggt ccctatctgc 2580 cgtgggcgtt ggatacttga acaggagcct gctcctagta cgagaggacc ggagtggacg 2640 tacctctggt gtaccggttg tcatgccaat ggcattgccg ggtagctaag tacggaagag 2700 ataaccgctg aaggcatcta agcggaaact cgtctgaaga ttaggtatcc cgggactaga 2760 tccccctgaa gggtcgttcg agaccaggac gttgataggt cgggtgtgga agcgcagtaa 2820 tgcgttaagc taaccgatac taattgcccg tgaggcttga tcct 2864 66 2878 DNA Burkholderia cepacia 66 ggtcaagcga acaagtgcat gtggtggatg ccttggcgat cacaggcgat gaaggacgcg 60 gtagcctgcg aaaagctacg gggagctggc aaacaagctt tgatccgtag atgtccgaat 120 ggggaaaccc actccttttg gagtatccat ggctgaatac ataggccatg cgaaggaacg 180 cggtgaactg aaacatctaa gtaaccgcag gaaaagaaat caaccgagat tcccaaagta 240 gtggcgagcg aaatgggatg agccttgcac tctttatttg tattgttagc cgaacgctct 300 ggaaagtgcg gccatagcag gtgatagccc tgtaggcgaa aacagtatga aagaactagg 360 tgtgcgacaa gtagggcggg acacgtgaaa tcctgtctga agatgggggg accatcctcc 420 aaggctaaat actcgtgatc gaccgatagt gaaccagtac cgtgagggaa aggcgaaaag 480 aaccccggga ggggagtgaa atagatcctg aaaccgcatg catacaaaca gtcggagcct 540 cgtaaggggt gacggcgtac cttttgtata atgggtcagc gacttacgtt cagtagcaag 600 cttaaccgta tagggcaggc gtaggaaagg agtccgaata gggcgttcag ttgctgggcg 660 tagacccgaa accaggtgat ctatccatgg ccaggatgaa ggtgcggtaa cacgtactgg 720 aggtccgaac ccactaacgt tgaaaagtta ggggatgagc tgtggatagg ggtgaaaggc 780 taaacaaacc tggaaatagc tggttctctc cgaaaactat ttaggtagtg cctcgtgtct 840 caccttcggg ggtagagcac tgtcatggtt ggggggtcta ttgcagatta ccccgccata 900 gcaaactccg aataccgaag agtgcaatca cgggagacag acatcgggtg ctaacgtccg 960 gtgtcaagag ggaaacaacc cagaccgcca gctaaggtcc ccaaatatag ctaagtggga 1020 aacgaagtgg gaaggctaaa acagtcagga ggttggctta gaagcagcca ccctttaaag 1080 aaagcgtaat agctcactga tcgagtcgtc ctgcgcggaa gatgtaacgg ggctaagcta 1140 tataccgaag ctgcggatgc gtgctttgca cgatggtagg agagcgttcc gtaagcctgc 1200 gaaggtgcct tgtaaagggt gctggaggta tcggaagtgc gaatgctgac atgagtagcg 1260 ataaaggggg tgaaaggccc cctcgccgta agcccaaggt ttcctacgca acgttcatcg 1320 gcgtagggtg agtcggcccc taaggcgagg cagaaatgcg tagctgatgg gaagcaggtc 1380 aatattcctg caccattgtt agatgcgatg gggggacgga tcgcggaagg ttgtccgggt 1440 gttggaagtc ccggtcgctg cattggagaa ggcgcttagg caaatccggg cgcagaattc 1500 aagggtgtgg cgcgagctcc ttcgggagcg aagcaattgg aagtggttcc aagaaaagcc 1560 tctaagcttc agtctaacga tgaccgtacc gcaaaccgac acaggtgggc gagatgagta 1620 ttctaaggcg cttgagagaa ctcgggagaa ggaactcggc aaattggtac cgtaacttcg 1680 ggataaggta cgcccttgta gcttgactgg cctgcgccag gagggtgaag gggttgcaat 1740 aaactggtgg ctgcgactgt ttaataaaaa cacagcactc tgcaaacacg aaagtggacg 1800 tatagggtgt gacgcctgcc cggtgccgga agattaaatg atggggtgca agctcttgat 1860 tgaagtcccg gtaaacggcg gccgtaacta taacggtcct aaggtagcga aattccttgt 1920 cgggtaagtt ccgacctgca cgaatggcgt aacgatggcc acactgtctc ctcccgagac 1980 tcagcgaagt tgaagtgttt gtgatgatgc aatctacccg cggctagacg gaaagacccc 2040 atgaaccttt actgtagctt tgcattggac tttgaaccga tctgtgtagg ataggtggga 2100 ggctatgaaa ccggaacgct agtttcggtg gagccgtcct tgaaatacca ccctggtttg 2160 tttgaggttc taaccttggc ccgtgatccg ggtcggggac agtgcatggt aggcagtttg 2220 actggggcgg tctcctccca aagcgtaacg gaggagtacg aaggtacgct aggtacggtc 2280 ggaaatcgtg ctgatagtgc aatggcataa gcgtgcttaa ctgcgagacc gacaagtcga 2340 gcaggtgcga aagcaggtca tagtgatccg gtggttctgt atggaagggc catcgctcaa 2400 cggataaaag gtactctggg gataacaggc tgataccgcc caagagttca tatcgacggc 2460 ggtgtttggc acctcgatgt cggctcatct catcctgggg ctgtagccgg tcccaagggt 2520 atggctgttc gccatttaaa gaggtacgtg agctgggttt aaaacgtcgt gagacagttt 2580 ggtccctatc tgccgtgggc gttggatatt tgaagggggc tgctcctagt acgagaggac 2640 cggagtggac gaacctctgg tgtaccggtt gtcacgccag tggcatcgcc gggtagctat 2700 gttcggaaga gataaccgct gaaagcatct aagcgggaaa ctcgccttaa gatgagatat 2760 ccctggggac tagatcccct tgaagggtcg ttcgagacca ggacgttgat aggtcaggtg 2820 tgtaagcgca gtaatgcgtt cagctaactg atactaattg cccgtaaggc ttgatcct 2878 67 2882 DNA Burkholderia mallei 67 ggtcaagcga acaagtgcat gtggtggatg ccttggcgat cacaggcgat gaaggacgcg 60 gtagcctgcg aaaagctacg gggagctggc aaacgagctt tgatccgtag atgtccgaat 120 ggggaaaccc ggcccttttg ggtcatccta gactgaatac ataggtctag tgaggcgaac 180 gcggtgaact gaaacatcta agtaaccgca ggaaaagaaa tcaaccgaga ttcccaaagt 240 agtggcgagc gaaatgggaa gagcctgtac tctttatttg tattgttagc cgaacgctct 300 ggaaagtgcg gccatagcag gtgatagccc tgtaggcgaa aacagtatga aagaactagg 360 tgtacgacaa gtagggcggg acacgtgaaa tcctgtctga agatgggggg accatcctcc 420 aaggctaaat actcgtgatc gaccgatagt gaaccagtac cgtgagggaa aggcgaaaag 480 aaccccggga ggggagtgaa atagatcctg aaaccgcatg catacaaaca gtcggagcct 540 cttcgggggt gacggcgtac cttttgtata atgggtcagc gacttacgtt cagtagcaag 600 cttaaccgaa tagggcaggc gtagcgaaag cgagtccgaa tagggcgttc agttgctggg 660 cgtagacccg aaaccaggtg atctatccat ggccaggatg aaggtgcggt aacacgtact 720 ggaggtccga acccactaac gttgaaaagt taggggatga gctgtggata ggggtgaaag 780 gctaaacaaa cctggaaata gctggttctc tccgaaaact atttaggtag tgcctcgtgt 840 ctcaccttcg ggggtagagc actgtcatgg ttggggggtc tattgcagat taccccgcca 900 tagcaaactc cgaataccga agagtgcaat cacgggagac agacatcggg tgctaacgtc 960 cggtgtcaag agggaaacaa cccagaccgc cagctaaggt ccccaaatat ggctaagtgg 1020 gaaacgaagt gggaaggcta aaacagtcag gaggttggct tagaagcagc caccctttaa 1080 agaaagcgta atagctcact gatcgagtcg tcctgcgcgg aagatgtaac ggggctaagc 1140 catataccga agctgcggat gcgagctagt ctcgcatggt aggagagcgt tccgtaagcc 1200 tgcgaaggtg cgttgaaaag cgtgctggag gtatcggaag tgcgaatgct gacatgagta 1260 gcgataaagg gggtgaaagg ccccctcgcc gtaagcccaa ggtttcctac gcaacgttca 1320 tcggcgtagg gtgagtcggc ccctaaggcg aggcagaaat gcgtagctga tgggaagcag 1380 gtcaatattc ctgcaccgtc gttagatgcg atggggggac ggatcgcgga aggttgtccg 1440 ggtgttggaa gtcccggtcg ctgcattgga gaaggcgctt aggcaaatcc gggcgcagga 1500 ttcaagggtg tggcgcgagc tccttcggga gcgaagcaat tggaagtggt tccaagaaaa 1560 gcctctaagc ttcagtctaa cgatgaccgt accgcaaacc gacacaggtg ggcgagatga 1620 gtattctaag gcgcttgaga gaactcggga gaaggaactc ggcaaattgg taccgtaact 1680 tcgggataag gtacgccctg gtagcttgac tggcctgcgc cagaagggtg aaggggttgc 1740 aataaactgg tggctgcgac tgtttaataa aaacacagca ctctgcaaac acgaaagtgg 1800 acgtataggg tgtgacgcct gcccggtgcc ggaagattaa atgatggggt gcaagctctt 1860 gattgaagtc ccggtaaacg gcggccgtaa ctataacggt cctaaggtag cgaaattcct 1920 tgtcgggtaa gttccgacct gcacgaatgg cgtaacgatg gccacactgt ctcctcccga 1980 gactcagcga agttgaagtg tttgtgatga tgcaatctac ccgcggctag acggaaagac 2040 cccatgaacc tttactgtag ctttgcattg gactttgaac cgatctgtgt aggataggtg 2100 ggaggctatg aaaccggaat gctagtttcg gtggagccgt ccttgaaata ccaccctggt 2160 ttgtttgagg ttctaacctt ggcccgtgat ccgggtcggg gacagtgcat ggtaggcagt 2220 ttgactgggg cggtctcctc ccaaagcgta acggaggagt acgaaggtac gctaggtacg 2280 gtcggaaatc gtgctgatag tgcaatggca taagcgtgct taactgcgag accgacaagt 2340 cgagcaggtg cgaaagcagg tcatagtgat ccggtggttc tgtatggaag ggccatcgct 2400 caacggataa aaggtactct ggggataaca ggctgatacc gcccaagagt tcatatcgac 2460 ggcggtgttt ggcacctcga tgtcggctca tctcatcctg gggctgtagc cggtcccaag 2520 ggtatggctg ttcgccattt aaagaggtac gtgagctggg tttaaaacgt cgtgagacag 2580 tttggtccct atctgccgtg ggcgttggaa gtttgaaggg ggctgctcct agtacgagag 2640 gaccggagtg gacgaacctc tggtgtaccg gttgtgacgc cagtcgcatc gccgggtagc 2700 tatgttcgga agagataacc gctgaaagca tctaagcggg aaactcgcct taagatgaga 2760 cttccccggg gacttgatcc ccttgaaggg tcgttcgaga ccaggacgtt gataggtcgg 2820 gtgtgtaagc gcagtaatgc gttcagctaa ccgatactaa ttgcccgtac ggcttgatcc 2880 ta 2882 68 2882 DNA Burkholderia pseudomallei 68 ggtcaagcga acaagtgcat gtggtggatg ccttggcgat cacaggcgat gaaggacgcg 60 gtagcctgcg aaaagctacg gggagctggc aaacgagctt tgatccgtag atgtccgaat 120 ggggaaaccc ggcccttttg ggtcatccta gactgaatac ataggtctag tgaggcgaac 180 gcggtgaact gaaacatcta agtaaccgca ggaaaagaaa tcaaccgaga ttcccaaagt 240 agtggcgagc gaaatgggaa gagcctgtac tctttatttg tattgttagc cgaacgctct 300 ggaaagtgcg gccatagcag gtgatagccc tgtaggcgaa aacagtatga aagaactagg 360 tgtacgacaa gtagggcggg acacgtgaaa tcctgtctga agatgggggg accatcctcc 420 aaggctaaat actcgtgatc gaccgatagt gaaccagtac cgtgagggaa aggcgaaaag 480 aaccccggga ggggagtgaa atagatcctg aaaccgcatg catacaaaca gtcggagcct 540 cttcgggggt gacggcgtac cttttgtata atgggtcagc gacttacgtt cagtagcaag 600 cttaaccgaa tagggcaggc gtagcgaaag cgagtccgaa tagggcgttc agttgctggg 660 cgtagacccg aaaccaggtg atctatccat ggccaggatg aaggtgcggt aacacgtact 720 ggaggtccga acccactaac gttgaaaagt taggggatga gctgtggata ggggtgaaag 780 gctaaacaaa cctggaaata gctggttctc tccgaaaact atttaggtag tgcctcgtgt 840 ctcaccttcg ggggtagagc actgtcatgg ttggggggtc tattgcagat taccccgcca 900 tagcaaactc cgaataccga agagtgcaat cacgggagac agacatcggg tgctaacgtc 960 cggtgtcaag agggaaacaa cccagaccgc cagctaaggt ccccaaatat ggctaagtgg 1020 gaaacgaagt gggaaggcta aaacagtcag gaggttggct tagaagcagc caccctttaa 1080 agaaagcgta atagctcact gatcgagtcg tcctgcgcgg aagatgtaac ggggctaagc 1140 catataccga agctgcggat gcgagctagt ctcgcatggt aggagagcgt tccgtaagcc 1200 tgcgaaggtg cgttgaaaag cgtgctggag gtatcggaag tgcgaatgct gacatgagta 1260 gcgataaagg gggtgaaagg ccccctcgcc gtaagcccaa ggtttcctac gcaacgttca 1320 tcggcgtagg gtgagtcggc ccctaaggcg aggcagaaat gcgtagctga tgggaagcag 1380 gtcaatattc ctgcaccgtc gttagatgcg atggggggac ggatcgcgga aggttgtccg 1440 ggtgttggaa gtcccggtcg ctgcattgga gaaggcgctt aggcaaatcc gggcgcagga 1500 ttcaagggtg tggcgcgagc gctctagggc gcgaagcaat tggaagtggt tccaagaaaa 1560 gcctctaagc ttcagtctaa cgatgaccgt accgcaaacc gacacaggtg ggcgagatga 1620 gtattctaag gcgcttgaga gaactcggga gaaggaactc ggcaaattgg taccgtaact 1680 tcgggataag gtacgccctg gtagcttgac tggcctgcgc cagaagggtg aaggggttgc 1740 aataaactgg tggctgcgac tgtttaataa aaacacagca ctctgcaaac acgaaagtgg 1800 acgtataggg tgtgacgcct gcccggtgcc ggaagattaa atgatggggt gcaagctctt 1860 gattgaagtc ccggtaaacg gcggccgtaa ctataacggt cctaaggtag cgaaattcct 1920 tgtcgggtaa gttccgacct gcacgaatgg cgtaacgatg gccacactgt ctcctcccga 1980 gactcagcga agttgaagtg tttgtgatga tgcaatctac ccgcggctag acggaaagac 2040 cccatgaacc tttactgtag ctttgcattg gactttgaac cgatctgtgt aggataggtg 2100 ggaggctatg aaaccggaac gctagtttcg gtggagccgt ccttgaaata ccaccctggt 2160 ttgtttgagg ttctaacctt ggcccgtgat ccgggtcggg gacagtgcat ggtaggcagt 2220 ttgactgggg cggtctcctc ccaaagcgta acggaggagt acgaaggtac gctaggtacg 2280 gtcggaaatc gtgctgatag tgcaatggca taagcgtgct taactgcgag accgacaagt 2340 cgagcaggtg cgaaagcagg tcatagtgat ccggtggttc tgtatggaag ggccatcgct 2400 caacggataa aaggtactct ggggataaca ggctgatacc gcccaagagt tcatatcgac 2460 ggcggtgttt ggcacctcga tgtcggctca tctcatcctg gggctgtagc cggtcccaag 2520 ggtatggctg ttcgccattt aaagaggtac gtgagctggg tttaaaacgt cgtgagacag 2580 tttggtccct atctgccgtg ggcgttggaa gtttgaaggg ggctgctcct agtacgagag 2640 gaccggagtg gacgaacctc tggtgtaccg gttgtgacgc cagtcgcatc gccgggtagc 2700 tatgttcgga agagataacc gctgaaagca tctaagcggg aaactcgcct taagatgaga 2760 cttccccggg gacttgatcc ccttgaaggg tcgttcgaga ccaggacgtt gataggtcgg 2820 gtgtgtaagc gcagtaatgc gttcagctaa ccgatactaa ttgcccgtac ggcttgatcc 2880 ta 2882 69 2890 DNA Neisseria gonorrhoeae 69 ggtcaagtga ataagtgcat caggcggatg ccttggcgat gataggcgac gaaggacgtg 60 taagcctgcg aaaagcgcgg gggagctggc aataaagcta tgattccgcg atgtccgaat 120 ggggaaaccc actgcattct gtgcagtatc ctaagttgaa tacataggct tagagaagcg 180 aacccggaga actgaaccat ctaagtaccc ggaggaaaag aaatcaaccg agattccgca 240 agtagtggcg agcgaacgcg gaggagcctg tacgtaataa ctgtcgagat agaagaacaa 300 gctgggaagc ttgaccatag cgggtgacag tcccgtattc gaaatctcaa cagcggtact 360 aagcgtacga aaagtagggc gggacacgtg aaatcctgtc tgaatatggg gggaccatcc 420 tccaaggcta aatactcatc atcgaccgat agtgaaccag taccgtgagg gaaaggcgaa 480 aagaaccccg ggagggaagt gaaacagaac ctgaaacctg atgcatacaa acagtgggag 540 cgccctagtg gtgtgactgc gtaccttttg tataatgggt caacgactta cattcagtag 600 cgagcttaac cggatagggg aggcgtaggg aaaccgagtc ttaatagggc gatgagttgc 660 tgggtgtaga cccgaaaccg agtgatctat ccatggtcag gttgaaggtg ccgtaacagg 720 tactggagga ccgaacccac gcatgttgca aaatgcgggg atgagctgtg ggtaggggtg 780 aaaggctaaa caaactcgga gatagctggt tctccccgaa aactatttag gtagtgcctc 840 gagcaagaca ctgatggggg taaagcactg ttatggctag ggggttattg caacttacca 900 acccatggca aactcagaat accatcaagt ggttcctcgg gagacagaca gcgggtgcta 960 acgtccgttg tcaagaggga aacaacccag accgccggct aaggtcccaa atgatagatt 1020 aagtggtaaa cgaagtggga aggcacagac agccaggatg ttggcttaga agcagccatc 1080 atttaaagaa agcgtaatag ctcactggtc gagtcgtcct gcgcggaaga tgtaacgggg 1140 ctcaaatcta taaccgaagc tgcggatgcc ggtttaccgg catggtaggg gagcgttctg 1200 taggctgatg aaggtgcatt gtaaagtgtg ctggaggtat cagaagtgcg aatgttgaca 1260 tgagtagcga taaagcgggt gaaaagcccg ctcgccgaaa gcccaaggtt tcctacgcaa 1320 cgttcatcgg cgtagggtaa gtcggcccct aaggcgaggc agaaatgcgt agtcgatggg 1380 aaacaggtta atattcctgt acttgattca aatgcgatgt ggggacggag aaggttaggt 1440 tggcaagctg ttggaatagc ttgtttaagc cggtaggtgg aagacttagg caaatccggg 1500 ttttcttaac accgagaagt gatgacgagt gtctacggac acgaagcaac cgataccacg 1560 cttccaggaa aagccactaa gcttcagttt gaatcgaacc gtaccccaaa ccgacacagg 1620 tgggtaggat gagaattcta aggcgcttga gagaactcgg gagaaggaac tcggcaaatt 1680 gataccgtaa cttcgggaga aggtatgccc tctaaggtta aggacttgct ccgtaagccc 1740 cggagggtcg cagagaatag gtggctgcga ctgtttatta aaaacacagc actctgccaa 1800 cacgaaagtg gacgtatagg gtgtgacgcc tgcccggtgc cggaaggtta attgaagatg 1860 tgcaagcatc ggatcgaagc cccggtaaac ggcggccgta actataacgg tcctaaggta 1920 gcgaaattcc ttgtcgggta agttccgacc cgcacgaatg gcgtaacgat ggccacactg 1980 tctcctcccg agactcagcg aagttgaagt ggttgtgaag atgcaatcta cccgctgcta 2040 gacggaaaga ccccgtgaac ctttactgta gctttgcatt ggactttgaa gtcacttgtg 2100 taggataggt gggaggcttg gaagcagaga cgccagtctc tgtggagtcg tccttgaaat 2160 accaccctgg tgtctttgag gttctaaccc agacccgtca tccgggtcgg ggaccgtgca 2220 tggtaggcag tttgactggg gcggtctcct cccaaagcgt aacggaggag ttcgaaggtt 2280 acctaggtcc ggtcggaaat cggactgata gtgcaatggc aaaaggtagc ttaactgcga 2340 gaccgacaag tcgggcaggt gcgaaagcag gacatagtga tccggtggtt ctgtatggaa 2400 gggccatcgc tcaacggata aaaggtactc cggggataac aggctgattc cgcccaagag 2460 ttcatatcga cggcggagtt tggcacctcg atgtcggctc atcacatcct ggggctgtag 2520 tcggtcccaa gggtatggct gttcgccatt taaagtggta cgtgagctgg gtttaaaacg 2580 tcgtgagaca gtttggtccc tatctgcagt ggcgttggaa gtttgacggg gctgctccta 2640 gtacgagagg accggagtgg acgaacctct ggtgtaccgg ttgtaacgcc agttgcatag 2700 ccgggtagct aagttcggaa gagataagcg ctgaaagcat ctaagcgcga aactcgcctg 2760 aagatgagac ttcccttgcg gtttaaccgc actaaagggt cgttcgagac caggacgttg 2820 ataggtgggg tgtggaagcg cggtaacgcg tgaagctaac ccatactaat tgcccgtgag 2880 gcttgactct 2890 70 2891 DNA Neisseria meningitidis 70 gtcaagtgaa taagtgcatc aggtggatgc cttggcgatg ataggcgacg aaggacgtgt 60 aagcctgcga aaagcgcggg ggagctggca ataaagcaat gatcccgcga tgtccgaatg 120 gggaaaccca ctgcattctg tgcagtatcc taagttgaat acatagactt agagaagcga 180 acccggagaa ctgaaccatc taagtacccg gaggaaaaga aatcaaccga gattccgcaa 240 gtagtggcga gcgaacgcgg aggagcctgt acgtaataac tgtcgagata gaagaacaag 300 ctgggaagct tgaccatagt gggtgacagt cccgtattcg aaatctcaac agcggtacta 360 agcgtacgaa aagtagggcg gggcacgtga aatcctgtct gaatatgggg ggaccatcct 420 ccaaggctaa atactcatca tcgaccgata gtgaaccagt accgtgaggg aaaggcgaaa 480 agaaccccgg gaggggagtg aaacagaacc tgaaacctga tgcatacaaa cagtgggagc 540 gccctagtgg tgtgactgcg taccttttgt ataatgggtc aacgacttac attcagtagc 600 gagcttaacc gaatagggga ggcgtaggga aaccgagtct taatagggcg atgagttgct 660 gggtgtagac ccgaaaccga gtgatctatc catggccagg ttgaaggtgc cgtaacaggt 720 actggaggac cgaacccacg catgttgcaa aatgcgggga tgagctgtgg ataggggtga 780 aaggctaaac aaactcggag atagctggtt ctccccgaaa actatttagg tagtgcctcg 840 agcaagacac tgatgggggt aaagcactgt tatggctagg gggttattgc aacttaccaa 900 cccatggcaa actaagaata ccatcaagtg gttcctcggg agacagacag cgggtgctaa 960 cgtccgttgt caagagggaa acaacccaga ccgccagcta aggtcccaaa tgatagatta 1020 agtggtaaac gaagtgggaa ggcccagaca gccaggatgt tggcttagaa gcagccatca 1080 tttaaagaaa gcgtaatagc tcactggtcg agtcgtcctg cgcggaagat gtaacggggc 1140 tcaaatctat aaccgaagct gcggatgccg gtttaccggc atggtagggg agcgttctgt 1200 aggctgatga aggtgcattg taaagtgtgc tggaggtatc agaagtgcga atgttgacat 1260 gagtagcgat aaagcgggtg aaaagcccgc tcgccgaaag cccaaggttt cctgcgcaac 1320 gttcatcggc gtagggtgag tcggccccta aggcgaggca gaaatgcgta gtcgatggga 1380 aacaggttaa tattcctgta cttgattcaa atgcgatgtg gggacggaga aggttaggtt 1440 ggcaagctgt tggaatagct tgtttaagcc ggtaggtgga agacttaggc aaatccgggt 1500 cttcttaaca ccgagaagtg acgacgagtg tctacggaca cgaagcaacc gataccacgc 1560 ttccaggaaa agccactaag cttcagtttg aatcgaaccg taccgcaaac cgacacaggt 1620 gggcaggatg agaattctaa ggcgcttgag agaactcagg agaaggaact cggcaaattg 1680 ataccgtaac ttcgggagaa ggtatgccct ctaaggttaa ggacttgctc cgtaagcccc 1740 ggagggtcgc agagaatagg tggctgcgac tgtttattaa aaacacagca ctctgctaac 1800 acgaaagtgg acgtataggg tgtgacgcct gcccggtgct ggaaggttaa ttgaagatgt 1860 gagagcatcg gatcgaagcc ccagtaaacg gcggccgtaa ctataacggt cctaaggtag 1920 cgaaattcct tgtcgggtaa gttccgaccc gcacgaatgg cgtaacgatg gccacactgt 1980 ctcctcctga gactcagcga agttgaagtg gttgtgaaga tgcaatctac ccgctgctag 2040 acggaaagac cccgtgaacc tttactgtag ctttgcattg gactttgaag tcacttgtgt 2100 aggataggtg ggaggcttag aagcagagac gccagtctct gtggagccgt ccttgaaata 2160 ccaccctggt gtctttgagg ttctaaccca gacccgtcat ccgggtcggg gaccgtgcat 2220 ggtaggcagt ttgactgggg cggtctcctc ccaaagcgta acggaggagt tcgaaggtta 2280 cctaggtccg gtcggaaatc ggactgatag tgcaatggca aaaggtagct taactgcgag 2340 accgacaagt cgagcaggtg cgaaagcagg acatagtgat ccggtggttc tgtatggaag 2400 ggccatcgct caacggataa aaggtactcc ggggataaca ggctgattcc gcccaagagt 2460 tcatatcgac ggcggagttt ggcacctcga tgtcggctca tcacatcctg gggctgtagt 2520 cggtcccaag ggtatggctg ttcgccattt aaagtggtac gtgagctggg tttaaaacgt 2580 cgtgagacag tttggtccct atctgcagtg ggcgttggaa gtttgacggg ggctgctcct 2640 agtacgagag gaccggagtg gacgaacctc tggtgtaccg gttgtaacgc cagttgcata 2700 gccgggtagc taagttcgga agagataagc gctgaaagca tctaagcgcg aaactcgcct 2760 gaagatgaga cttcccttgc ggtttaaccg cactaaagag tcgttcgaga ccaggacgtt 2820 gataggtggg gtgtggaagc gcggtaacgc gtgaagctaa cccatactaa ttgctcgtga 2880 ggcttgactc t 2891 71 2891 DNA Pseudomonas aeruginosa 71 ggtcaagtga agaagcgcat acggtggatg ccttggcagt cagaggcgat gaaagacgtg 60 gtagcctgcg aaaagcttcg gggagtcggc aaacagactt tgatccggag atctctgaat 120 gggggaaccc acctaggata acctaggtat cttgtactga atccataggt gcaagaggcg 180 aaccagggga actgaaacat ctaagtaccc tgaggaaaag aaatcaaccg agattccctt 240 agtagtggcg agcgaacggg gattagccct taagcttcat tgattttagc ggaacgctct 300 ggaaagtgcg gccatagtgg gtgatagccc cgtacgcgaa aggatctttg aagtgaaatc 360 gagtaggacg gagcacgaga aactttgtct gaacatgggg ggaccatcct ccaaggctaa 420 atactactga ctgaccgata gtgaaccagt accgtgaggg aaaggcgaaa agaaccccgg 480 agaggggagt gaaatagaac ctgaaaccgt atgcgtacaa gcagtgggag cctacttgtt 540 aggtgactgc gtaccttttg tataatgggt cagcgactta tattcagtgg caagcttaac 600 cgtatagggt aggcgtagcg aaagcgagtc ttaatagggc gtttagtcgc tgggtataga 660 cccgaaaccg ggcgatctat ccatgagcag gttgaaggtt aggtaacact gactggagga 720 ccgaacccac tcccgttgaa aaggtagggg atgacttgtg gatcggagtg aaaggctaat 780 caagctcgga gatagctggt tctcctcgaa agctatttag gtagcgcctc atgtatcact 840 ctggggggta gagcactgtt tcggctaggg ggtcatcccg acttaccaaa ccgatgcaaa 900 ctccgaatac ccagaagtgc cgagcatggg agacacacgg cgggtgctaa cgtccgtcgt 960 gaaaagggaa acaacccaga ccgccagcta aggtcccaaa gttgtggtta agtggtaaac 1020 gatgtgggaa ggcttagaca gctaggaggt tggcttagaa gcagccaccc tttaaagaaa 1080 gcgtaatagc tcactagtcg agtcggcctg cgcggaagat gtaacggggc tcaaaccaca 1140 caccgaagct gcgggtgtca cgtaagtgac gcggtagagg agcgttctgt aagcctgtga 1200 aggtgagttg agaagcttgc tggaggtatc agaagtgcga atgctgacat gagtaacgac 1260 aatgggtgtg aaaaacaccc acgccgaaag accaagggtt cctgcgcaac gttaatcgac 1320 gcagggttag tcggttccta aggcgaggct gaaaagcgta gtcgatggga aacaggttaa 1380 tattcctgta cttctggtta ctgcgatgga gggacggaga aggctaggcc agcttggcgt 1440 tggttgtcca agtttaaggt ggtaggctga aatcttaggt aaatccgggg tttcaaggcc 1500 gagagctgat gacgagtcgt cttttagatg acgaagtggt tgatgccatg cttccaagaa 1560 aagcttctaa gcttcaggta accaggaacc gtaccccaaa ccgacacagg tggtcgggta 1620 gagaatacca aggcgcttga gagaactcgg gtgaaggaac taggcaaaat ggcaccgtaa 1680 cttcgggaga aggtgcgccg gctagggtga aggatttact ccgtaagctc tggctggtcg 1740 aagataccag gccgctgcga ctgtttatta aaaacacagc actctgcaaa cacgaaagtg 1800 gacgtatagg gtgtgacgcc tgcccggtgc cggaaggtta attgatgggg ttagcgcaag 1860 cgaagctctt gatcgaagcc ccggtaaacg gcggccgtaa ctataacggt cctaaggtag 1920 cgaaattcct tgtcgggtaa gttccgacct gcacgaatgg cgtaacgatg gcggcgctgt 1980 ctccacccga gactcagtga aattgaaatc gctgtgaaga tgcagtgtat ccgcggctag 2040 acggaaagac cccgtgaacc tttactgtag ctttgcactg gactttgagc ctgcttgtgt 2100 aggataggtg ggaggctttg aagcgtggac gccagttcgc gtggagccat ccttgaaata 2160 ccaccctggc atgcttgagg ttctaactct ggtccgtaat ccggatcgag gacagtgtat 2220 ggtgggcagt ttgactgggg cggtctcctc ctaaagagta acggaggagt acgaaggtgc 2280 gctcagaccg gtcggaaatc ggtcgcagag tataaaggca aaagcgcgct tgactgcgag 2340 acagacacgt cgagcaggta cgaaagtagg tcttagtgat ccggtggttc tgtatggaag 2400 ggccatcgct caacggataa aaggtactcc ggggataaca ggctgatacc gcccaagagt 2460 tcatatcgac ggcggtgttt ggcacctcga tgtcggctca tcacatcctg gggctgaagc 2520 cggtcccaag ggtatggctg ttcgccattt aaagtggtac gcgagctggg tttagaacgt 2580 cgtgagacag ttcggtccct atctgccgtg gacgtttgag atttgagagg ggctgctcct 2640 agtacgagag gaccggagtg gacgaacctc tggtgttccg gttgtcacgc cagtggcatt 2700 gccgggtagc tatgttcgga aaagataacc gctgaaagca tctaagcggg aaacttgcct 2760 caagatgaga tctcactggg aacttgattc ccctgaaggg ccgtcgaaga ctacgacgtt 2820 gataggctgg gtgtgtaagc gttgtgaggc gttgagctaa ccagtactaa ttgcccgtga 2880 ggcttgacca t 2891 72 2886 DNA Vibrio cholerae 72 ggttaagtga ctaagcgtac acggtggatg cctgggcagt cagaggcgat gaaggacgta 60 ctaacttgcg ataagcgcag ataaggcagt aagagccgtt tgagtctgcg atttccgaat 120 ggggaaaccc aactgcataa gcagttactg ttaactgaat acataggtta acagagcaaa 180 ccgggggaac tgaaacatct aagtaccccg aggagaagaa atcaaccgag attccggtag 240 tagcggcgag cgaacctgga ttagccctta agcactcggt gaagtaggtg aacaagctgg 300 aaagcttggc gatacagggt gatagccccg taaccgacgc ttcatcgagc gtgaaatcga 360 gtagggcggg acacgtgata tcctgtctga atatgggggg accatcctcc aaggctaaat 420 actcctgact gaccgatagt gaaccagtac cgtgaggaaa ggcgaaaaga acccctgtga 480 ggggagtgaa atagaacctg aaaccgtgta cgtacaagca gtaggagcac cttcgtggtg 540 tgactgcgta ccttttgtat aatgggtcag cgacttatat tcagtggcaa ggttaaccgt 600 ataggggagc cgtagcgaaa gcgagtctta actgggcgct cagtctctgg atatagaccc 660 gaaaccgggt gatctagcca tgggcaggtt gaaggttgag taacatcaac tggaggaccg 720 aaccgactaa tgttgaaaaa ttagcggatg acttgtggct aggggtgaaa ggccaatcaa 780 actcggagat agctggttct ccccgaaagc tatttaggta gcgcctcgga cgaatactac 840 tgggggtaga gcactgttaa ggctaggggg tcatcccgac ttaccaaccc tttgcaaact 900 ccgaatacca gtaagtacta tccgggagac acacggcggg tgctaacgtc cgtcgtggag 960 agggaaacaa cccagaccgc cagctaaggt cccaaagtat tgctaagtgg gaaacgatgt 1020 gggaaggctc agacagctag gatgttggct tagaagcagc catcatttaa agaaagcgta 1080 atagctcact agtcgagtcg gcctgcgcgg aagatgtaac ggggctaagc aatacaccga 1140 agctgcggca atatctttta gatattgggt aggggagcgt tctgtaagcc gttgaaggtg 1200 aatcgtaagg tttgctggag gtatcagaag tgcgaatgct gacatgagta acgacaaagg 1260 gggtgaaaaa cctcctcgcc ggaagaccaa gggttcctgt ccaacgttaa tcggggcagg 1320 gtgagtcgac ccctaaggtg aggccgaaag gcgtaatcga tgggaaacgg gttaatattc 1380 ccgtacttct gactattgcg atggggggac ggagaaggct aggtgggcca ggcgacggtt 1440 gtcctggttc aagtgcgtag gcttgagagt taggtaaatc cggctctctc taaggctgag 1500 acacgacgtc gagctactac ggtagtgaag tcattgatgc catgcttcca ggaaaagcct 1560 ctaagcttca gatagtcagg aatcgtaccc caaaccgaca caggtggtcg ggtagagaat 1620 accaaggcgc ttgagagaac tcgggtgaag gaactaggca aaatggtacc gtaacttcgg 1680 gagaaggtac gctcttgatg gtgaagtccc tcgcggatgg agctgacgag agtcgcagat 1740 accaggtggc tgcaactgtt tattaaaaac acagcactgt gcaaaatcgc aagatgacgt 1800 atacggtgtg acgcctgccc ggtgccggaa ggttaattga tggggttagc gcaagcgaag 1860 ctcttgatcg aagccccggt aaacggcggc cgtaactata acggtcctaa ggtagcgaaa 1920 ttccttgtcg ggtaagttcc gacctgcacg aatggcgtaa tgatggccac gctgtctcca 1980 cccgagactc agtgaaattg aaatcgctgt gaagatgcag tgtacccgcg gctagacgga 2040 aagaccccgt gaacctttac tacagcttgg cactgaacat tgaacctaca tgtgtaggat 2100 aggtgggagg ctatgaagac gtgacgccag ttgcgttgga gccgtccttg aaataccacc 2160 cttgtatgtt tgatgttcta acttagaccc gttatccggg ttgaggacag tgcctggtgg 2220 gtagtttgac tggggcggtc tcctcccaaa gagtaacgga ggagcacgaa ggtgggctaa 2280 tcacggttgg acatcgtgag gttagtgcaa tggcataagc ccgcttaact gcgagaatga 2340 cggttcgagc aggtgcgaaa gcaggtcata gtgatccggt ggttctgtat ggaagggcca 2400 tcgctcaacg gataaaaggt actccgggga taacaggctg ataccgccca agagttcata 2460 tcgacggcgg tgtttggcac ctcgatgtcg gctcatcaca tcctggggct gaagtcggtc 2520 ccaagggtat ggctgttcgc catttaaagt ggtacgcgag ctgggtttag aacgtcgtga 2580 gacagttcgg tccctatctg ccgtgggcgt tggaagattg aagggggctg ctcctagtac 2640 gagaggaccg gagtggacga acctctggtg ttcgggttgt gtcgccagac gcattgcccg 2700 gtagctaagt tcggaattga taagcgctga aagcatctaa gcgcgaagcg agccctgaga 2760 tgagtcttcc ctgacagttt aactgtccta aagggttgtt cgagactaga acgttgatag 2820 gcagggtgtg taagcgttgt gaggcgttga gctaacctgt actaattgcc cgtgaggctt 2880 aaccat 2886 73 2906 DNA Yersinia enterocolitica modified_base (1168)..(1178) N = A, C, G or T/U 73 ggttaagcga ccaagcgtac acggtggatg cctaggcagt cagaggcgat gaaggacgtg 60 ctaatctgcg aaaagcgtcg gtaaggtgat atgaaccgtt ataaccgacg atacccgaat 120 ggggaaaccc agtgcaattc gttgcactat tgcatggtga atacatagcc atgcaaggcg 180 aaccggggga actgaaacat ctaagtaccc cgaggaaaag aaatcaaccg agattccccc 240 agtagcggcg agcgaacggg gaggagccca gaacctgaat cagcgtatgt gttagtggaa 300 gcgtctggaa agtcgcacgg tacagggtga tagtcccgta cacaaaaatg catatgttgt 360 gagttcgatg agtagggcgg gacacgtgac atcctgtctg aatatggggg gaccatcctc 420 caaggctaaa tactcctgac tgaccgatag tgaaccagta ccgtgaggga aaggcgaaaa 480 gaaccccggc gaggggagtg aaacagaacc tgaaaccgtg tacgtacaag cagtgggagc 540 accttcgtgg tgtgactgcg taccttttgt ataatgggtc agcgacttat attttgtagc 600 aaggttaacc gaatagggga gccgtaggga aaccgagtct taactgggcg aatagttgca 660 aggtatagac ccgaaacccg gtgatctagc catgggcagg ttgaaggttg ggtaacacta 720 actggaggac cgaaccgact aatgttgaaa aattagcgga tgacttgtgg ctgggggtga 780 aaggccaatc aaaccgggag atagctggtt ctccccgaaa gctatttagg tagcgcctcg 840 tgaactcatc ttcgggggta gagcactgtt tcggctaggg ggtcatcccg acttaccaaa 900 ccgatgcaaa ctccgaatac cgaagaatgt tatcacggga gacacacggc gggtgctaac 960 gtccgtcgtg aagagggaaa caacccagac cgccagctaa ggtcccaaag tcatggttaa 1020 gtgggaaacg atgtgggaag gcacagacag ccaggatgtt ggcttagaag cagccatcat 1080 ttaaagaaag cgtaatagct cactggtcga gtcggcctgc gcggaagatg taacggggct 1140 aaaccatgca ccgaagctgc ggcagcgnnn nnnnnnnnnn nnnnnnnngg ggagcgttct 1200 gtaagccgtt gaaggtgacc tgtgagggtt gctggaggta tcagaagtgc gaatgctgac 1260 ataagtaacg ataatgcggg tgaaaaaccc gcacgccgga agaccaaggg ttcctgtcca 1320 acgttaatcg gggcagggtg agtcgacccc taaggcgagg ctgaaaggcg tagtcgatgg 1380 gaaacaggtt aatattcctg tacttggtgt tactgcgaag gggggacgga gaaggctatg 1440 ctagccgggc gacggttgtc ccggtttaag catgtaggcg gagtgaccag gtaaatccgg 1500 ttgcttatca acgctgaggt gtgatgacga gtcactacgg tgatgaagta gttgatgcca 1560 tgcttccagg aaaagcctct aagcatcagg taacatgaaa tcgtacccca aaccgacaca 1620 ggtggtcagg tagagaatac tcaggcgctt gagagaactc gggtgaagga actaggcaaa 1680 atggtgccgt aacttcggga gaaggcacgc tgacacgtag gtgaagcggt ttacccgtgg 1740 agctgaagtc agtcgaagat accagctggc tgcaactgtt tattaaaaac acagcactgt 1800 gcaaacacga aagtggacgt atacggtgtg acgcctgccc ggtgctggaa ggttaattga 1860 tggggtcagc gcaagcgaag ctcttgatcg aagccccggt aaacggcggc cgtaactata 1920 acggtcctaa ggtagcgaaa ttccttgtcg ggtaagttcc gacctgcacg aatggcgtaa 1980 tgatggccag gctgtctcca cccgagactc agtgaaattg aactcgctgt gaagatgcag 2040 tgtacccgcg gcaagacgga aagaccccgt gaacctttac tatagcttga cactgaacat 2100 tgagccttga tgtgtaggat aggtgggagg catagaagtg tggacgccag tctgcatgga 2160 gccaaccttg aaataccacc ctttaatgtt tgatgttcta actcggcccc gtaatccggg 2220 gtgaggacag tgtcaggtgg gtagtttgac tggggcggtc tcctcccaaa gagtaacgga 2280 ggagcacgaa ggttagctaa tcacggtcgg acatcgtgag gttagtgcaa aggcataagc 2340 tagcttcact gcgagagtga cggctcgagc aggtacgaaa gtaggtctta gtgatccggt 2400 ggttctgaat ggaagggcca tcgctcaacg gataaaaggt actccgggga taacaggctg 2460 ataccgccca agagttcata tcgacggcgg tgtttggcac ctcgatgtcg gctcatcaca 2520 tcctggggct gaagtaggtc ccaagggtat ggctgttcgc catttaaagt ggtacgcgag 2580 ctgggtttag aacgtcgtga gacagttcgg tccctatctg ccgtgggcgy tggarraytg 2640 agrggggctg ctcctagtac gagaggaccg gagtggacgm atcactggtg ttcgggttgt 2700 catgccaatg gcaytgcccg gtagctaaat kcggaagaga taasygctga aagcatctaa 2760 gcrsgaaact tgccycgaga tgagttctcc ctgagactac aagtctcctg aaggaacgtt 2820 gaagacgacg acgttgatag gcygggtgtg taagcgcgag ttggcgttga gctaaccggt 2880 actaatgaac cgtgaggctt aacctt 2906 

What is claimed is:
 1. A method for depleting or isolating a targeted nucleic acid from a sample comprising: a) incubating the sample with a first bridging oligonucleotide comprising (1) at least one bridging region comprising at least 5 nucleic acid residues and (2) at least one targeting region comprising at least 5 nucleic acid residues, under conditions allowing hybridization between the first targeting region and the targeted nucleic acid; b) incubating the first bridging oligonucleotide with a capture oligonucleotide comprising a nonreacting structure and a capture region comprising at least 5 nucleic acid residues, under conditions allowing hybridization between the bridging region and the capture region; and c) isolating the targeted nucleic acid from the remainder of the sample.
 2. The method of claim 1 wherein the targeted nucleic acid is rRNA.
 3. The method of claim 2, wherein the rRNA is prokaryotic 16S, prokaryotic 23S, eukaryotic 17S or 18S, or eukaryotic 28S rRNA.
 4. The method of claim 3, wherein the rRNA comprises the sequence of SEQ ID NO:23, SEQ ID NO:24, SEQ ID NO:25, SEQ ID NO:26, SEQ ID NO:27, SEQ ID NO:28, SEQ ID NO:29, SEQ ID NO:30, SEQ ID NO:31, SEQ ID NO:32, SEQ ID NO:33, SEQ ID NO:34, SEQ ID NO:35, SEQ ID NO:36, SEQ ID NO:37, SEQ ID NO:38, SEQ ID NO:39, SEQ ID NO:40, SEQ ID NO:41, SEQ ID NO:42, SEQ ID NO:43, SEQ ID NO:44, SEQ ID NO:45, SEQ ID NO:46, SEQ ID NO:47, SEQ ID NO:48, SEQ ID NO:49, SEQ ID NO:50, SEQ ID NO:51, SEQ ID NO:52, SEQ ID NO:53, SEQ ID NO:54, SEQ ID NO:55, SEQ ID NO:56, SEQ ID NO:57, SEQ ID NO:58, SEQ ID NO:59, SEQ ID NO:60, SEQ ID NO:61, SEQ ID NO:62, SEQ ID NO:63, SEQ ID NO:64, SEQ ID NO:65, SEQ ID NO:66, SEQ ID NO:67, SEQ ID NO:68, SEQ ID NO:69, SEQ ID NO:71, SEQ ID NO:72, or SEQ ID NO:73.
 5. The method of claim 1, wherein the sample comprises eukaryotic nucleic acid.
 6. The method of claim 1, wherein the sample comprises prokaryotic nucleic acid.
 7. The method of claim 6, wherein the prokaryotic nucleic acid is from a gram positive bacterium.
 8. The method of claim 6, wherein the prokaryotic nucleic acid is from a gram negative bacterium.
 9. The method of claim 1, wherein the bridging region, targeting region, or capture region comprises at least 10 nucleic acid residues.
 10. The method of claim 9, wherein the bridging region, targeting region, or capture region comprises at least 15 nucleic acid residues.
 11. The method of claim 10, wherein the bridging region, targeting region, or capture region comprises at least 20 nucleic acid residues.
 12. The method of claim 1, wherein the bridging region or the capture region is polypurine or polypyrimidine.
 13. The method of claim 12, wherein the bridging region is polypurine and the capture region is polypyrimidine.
 14. The method of claim 1, further comprising incubating the sample with a second bridging oligonucleotide comprising (1) at least one bridging region comprising at least 5 nucleic acid residues and (2) at least one targeting region comprising at least 5 nucleic acid residues, under conditions allowing hybridization between the targeting region of the second bridging oligonucleotide and the targeted nucleic acid.
 15. The method of claim 14, wherein the targeting region of the first bridging oligonucleotide is complementary to the sequence of a targeted nucleic acid and the targeting region of the second bridging oligonucleotide is complementary to a different sequence of a targeted nucleic acid.
 16. The method of claim 15, wherein the targeting region of the first bridging oligonucleotide and the targeting region of the second bridging oligonucleotide are complementary to the same targeted nucleic acid.
 17. The method of claim 15, wherein the targeting region of the first bridging oligonucleotide and the targeting region of the second bridging oligonucleotide are complementary to different targeted nucleic acids.
 18. The method of claim 17, wherein the targeting region of the first bridging oligonucleotide is complementary to a sequence of the largest rRNA molecule and the targeting region of the second bridging oligonucleotide is complementary to a sequence of the second largest rRNA molecule in the sample.
 19. The method of claim 14, wherein the targeting region of the first or second bridging oligonucleotide hybridizes to a sequence located between 100 and 5000 residues of the 5′ or 3′ end of the targeted nucleic acid.
 20. The method of claim 19, wherein the targeting region of the first or second bridging oligonucleotide hybridizes to a sequence located between 150 and 4000 residues of the 5′ or 3′ end of the targeted nucleic acid.
 21. The method of claim 20, wherein the targeting region of the first or second bridging oligonucleotide hybridizes to a sequence located between 200 and 3000 residues of the 5′ or 3′ end of the targeted nucleic acid.
 22. The method of claim 21, wherein the targeting region of the first or second bridging oligonucleotide hybridizes to a sequence located between 250 and 2000 residues of the 5′ or 3′ end of the targeted nucleic acid.
 23. The method of claim 22, wherein the targeting region of the first or second bridging oligonucleotide hybridizes to a sequence located between 300 and 1500 residues of the 5′ or 3′ end of the targeted nucleic acid.
 24. The method of claim 23, wherein the targeting region of the first or second bridging oligonucleotide hybridizes to a sequence located between 350 and 1000 residues of the 5′ or 3′ end of the targeted nucleic acid.
 25. The method of claim 24, wherein targeting region of the first or second bridging oligonucleotide hybridizes to a sequence located between 400 and 900 residues of the 5′ or 3′ end of the targeted nucleic acid.
 26. The method of claim 25, wherein the targeting region of the first or second bridging oligonucleotide hybridizes to a sequence located between 450 and 800 residues of the 5′ or 3′ end of the targeted nucleic acid.
 27. The method of claim 26, wherein the targeting region of the first or second bridging oligonucleotide hybridizes to a sequence located between 500 and 700 residues of the 5′ or 3′ end of the targeted nucleic acid.
 28. The method of claim 14, wherein the targeting region of the first or second bridging oligonucleotide hybridizes to a sequence at the 3′ or 5′ end of the targeted nucleic acid.
 29. The method of claim 14, wherein the targeting region of the first or second bridging oligonucleotide hybridizes to a sequence not within 100 residues from the 3′ or 5′ end of the targeted nucleic acid.
 30. The method of claim 14, wherein targeting region of the first or second bridging oligonucleotide hybridizes to a sequence not within 200 residues from the 3′ or 5′ end of the targeted nucleic acid.
 31. The method of claim 14, wherein the targeting region of the first or second bridging oligonucleotide hybridizes to a sequence not within 400 residues from the 3′ or 5′ ends of the targeted nucleic acid.
 32. The method of claim 14, wherein the targeting region of the first or second bridging oligonucleotide comprises SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12, SEQ ID NO:13, SEQ ID NO:14, SEQ ID NO:15, SEQ ID NO:16, SEQ ID NO:17, SEQ ID NO:18, SEQ ID NO:19, SEQ ID NO:20, SEQ ID NO:21, or SEQ ID NO:22.
 33. The method of claim 1, wherein the bridging oligonucleotide comprises a second targeting region comprising at least 5 nucleic acid residues complementary to a different sequence than the sequence to which the first targeting region is complementary.
 34. The method of claim 33, wherein the first targeting region is complementary to a different targeting nucleic acid than the second targeting region is.
 35. The method of claim 1, wherein the first bridging oligonucleotide comprises two bridging regions.
 36. The method of claim 1, wherein the bridging oligonucleotide or the capture oligonucleotide is RNA, DNA, LNA, iso-bases, or a peptide nucleic acid.
 37. The method of claim 1, further comprising washing the capture oligonucleotide after incubation with the sample and the bridging oligonucleotide.
 38. The method of claim 1, wherein a) and b) are performed at the same temperature.
 39. The method of claim 1, wherein a) and b) are performed at a different temperature.
 40. The method of claim 38, wherein a) and b) are performed at the same time.
 41. The method of claim 1, wherein the nonreacting structure comprises a bead comprising plastic, glass, teflon, silica, a magnet, cellulose, latex, polystyrene, nylon, cellulose, nitrocellulose, polymethacrylate, polyvinylchloride, or styrene-divinylbenzene
 42. The method of claim 41, wherein isolating the targeted nucleic acid away from the sample comprises exposing the sample with the capture oligonucleotide to a magnetic field.
 43. The method of claim 1, wherein the nonreacting structure is cellulose.
 44. The method of claim 1, wherein the nonreacting structure is biotin.
 45. The method of claim 44, wherein isolating the targeted nucleic acid comprises incubating the sample with streptavidin or avidin.
 46. The method of claim 1, wherein the sample, capture oligonucleotide, and bridging oligonucleotide are incubated in a buffer comprising TMAC or TEAC.
 47. The method of claim 1, further comprising: d) discarding the portion of the sample that hybridizes to the capture oligonucleotide.
 48. The method of claim 2, further comprising: d) discarding the targeted rRNA nucleic acid; and e) producing cDNA using mRNA in the remainder of the sample.
 49. The method of claim 48, further comprising: f) attaching the cDNA to a solid support, wherein a nucleic acid array is created.
 50. The method of claim 49, wherein the solid support is plastic, glass, or nylon.
 51. The method of claim 50, wherein the solid support is a plate.
 52. The method of claim 51, wherein the plate is a multiple-well plate.
 53. The method of claim 48, further comprising: f) contacting a nucleic acid array with the cDNA.
 54. A method for depleting rRNA from a sample comprising: a) incubating the sample with at least a first (1) bridging oligonucleotide comprising a bridging region comprising a poly-purine region of at least 5 residues and a targeting region comprising at least 5 contiguous nucleic acid residues complementary to a sequence of an rRNA molecule and a (2) capture oligonucleotide comprising a magnetic bead and a capture region comprising a poly-pyrimidine region of at least 5 residues, under conditions to allow hybridization between the bridging oligonucleotide and the capture oligonucleotide and the bridging oligonucleotide and the rRNA; b) incubating the sample with a magnetic bead; and c) isolating the magnetic bead.
 55. A kit, in a suitable container means, comprising: a) a capture oligonucleotide comprising a capture region and a magnetic bead; and b) at least a first bridging oligonucleotide comprising (1) at least one bridging region complementary to all or part of the capture region of the capture oligonucleotide and a (2) at least one targeting region comprising 10 contiguous nucleic acids complementary to a sequence of an rRNA.
 56. The kit of claim 55, wherein the first bridging oligonucleotide comprises a second targeting region.
 57. The kit of claim 56, wherein the first and second targeting regions have the same nucleic acid sequence.
 58. The kit of claim 56, wherein the first and second targeting regions have different nucleic acid sequences.
 59. The kit of claim 58, wherein the first targeting region is complementary to a sequence of an eukaryotic rRNA and the second targeting region is complementary to a sequence of a prokaryotic rRNA.
 60. The kit of claim 58, wherein the first targeting region is complementary to a sequence of an eukaryotic rRNA and the second targeting region is complementary to a sequence of a different eukaryotic rRNA than the first targeting region.
 61. The kit of claim 58, wherein the first targeting region is complementary to a sequence of a prokaryotic rRNA and the second targeting region is complementary to a sequence of a different prokaryotic rRNA than the first targeting region.
 62. The kit of claim 55, further comprising a second bridging oligonucleotide comprising (1) at least one bridging region complementary to all or part of the capture region of the capture oligonucleotide and a (2) at least one targeting region comprising 10 contiguous nucleic acids complementary to a sequence of an rRNA.
 63. The kit of claim 62, wherein the targeting region of the second bridging oligonucleotide is complementary to a sequence of the same rRNA as the first targeting region.
 64. The kit of claim 62, wherein the targeting region of the first bridging oligonucleotide is complementary to a sequence of the largest rRNA and the targeting region of the second bridging oligonucleotide is complementary to a sequence of the second largest rRNA in the sample.
 65. The kit of claim 62, wherein the targeting region of the first bridging oligonucleotide is complementary to a sequence of an eukaryotic rRNA and the targeting region of the bridging oligonucleotide is complementary to a sequence of a prokaryotic rRNA.
 66. The kit of claim 64, wherein the targeting region of the first bridging oligonucleotide is complementary to a sequence of an eukaryotic 28S rRNA and the targeting region of the second bridging oligonucleotide is complementary to a sequence of a eukaryotic 17S or 18S rRNA.
 67. The kit of claim 64, wherein the targeting region of the first bridging oligonucleotide is complementary to a sequence of a prokaryotic 23S rRNA and the targeting region of the second bridging oligonucleotide is complementary to a sequence of a prokaryotic 16S rRNA.
 68. The kit of claim 64, wherein the targeting region of the first bridging oligonucleotide is complementary to a sequence of an eukaryotic 28S rRNA and the targeting region of the second bridging oligonucleotide is complementary to a sequence of a prokaryotic 23S rRNA.
 69. The kit of claim 62, further comprising a third bridging oligonucleotide comprising (1) at least one bridging region complementary to all or part of the capture region of the capture oligonucleotide and a (2) at least one targeting region comprising 10 contiguous nucleic acids complementary to a sequence of an rRNA.
 70. The kit of claim 69, wherein the targeting region of the third bridging oligonucleotide is complementary to a sequence of a prokaryotic 23S rRNA.
 71. The kit of claim 69, wherein the targeting region of the third bridging oligonucleotide is complementary to a sequence of a eukaryotic 18S rRNA.
 72. The kit of claim 69, further comprising a fourth bridging oligonucleotide comprising (1) at least one bridging region complementary to all or part of the capture region of the capture oligonucleotide and a (2) at least one targeting region comprising 10 contiguous nucleic acids complementary to a sequence of an rRNA.
 73. The kit of claim 72, wherein (i) the targeting region of the first bridging oligonucleotide is complementary to a sequence of a prokaryotic 16S rRNA, (ii) the targeting region of the second bridging oligonucleotide is complementary to a sequence of a prokaryotic 23S rRNA, (iii) the targeting region of the third bridging oligonucleotide is complementary to a sequence of a eukaryotic 18S rRNA, and (iv) the targeting region of the fourth bridging oligonucleotide is complementary to a sequence of a eukaryotic 28S rRNA,
 74. The kit of claim 55, wherein the first targeting region of the bridging oligonucleotide comprises SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12, SEQ ID NO:13, SEQ ID NO:14, SEQ ID NO:15, SEQ ID NO:16, SEQ ID NO:17, SEQ ID NO:18, SEQ ID NO:19, SEQ ID NO:20, SEQ ID NO:21, or SEQ ID NO:22.
 75. The kit of claim 55, further comprising a buffer comprising TMAC or TEAC.
 76. The kit of claim 55, further comprising a magnetic stand.
 77. The kit of claim 55, further comprising: c) a solid support for preparing a nucleic acid array.
 78. A bridging oligonucleotide comprising a (1) bridging region comprising a polypyrimidine or polypurine stretch and a (2) targeting region comprising at least 10 contiguous nucleic acid residues complementary to a sequence of an rRNA.
 79. The oligonucleotide of claim 78, wherein the rRNA is eukaryotic.
 80. The oligonucleotide of claim 79, wherein the rRNA is the 28S rRNA.
 81. The oligonucleotide of claim 78, wherein the rRNA is prokaryotic.
 82. The oligonucleotide of claim 81, wherein the rRNA is the 23S rRNA.
 83. A method for depleting or isolating a targeted rRNA from a sample comprising: a) obtaining the kit of claim 55; b) incubating the sample with the bridging oligonucleotide under conditions allowing hybridization between the targeting region and the targeted rRNA; c) incubating the bridging oligonucleotide with the capture oligonucleotide under conditions allowing hybridization between the bridging region and the capture region; and d) isolating the targeted rRNA from the remainder of the sample by incubating the sample with a magnetic field.
 84. The method of claim 83, further comprising: e) obtaining the remainder of the sample enriched for mRNA; f) preparing cDNA from the mRNA.
 85. The method of claim 84, further comprising: g) constructing a nucleic acid array with the cDNA. 